Science.gov

Sample records for acquired mass spectra

  1. Clustering and Filtering Tandem Mass Spectra Acquired in Data-Independent Mode

    NASA Astrophysics Data System (ADS)

    Pak, Huisong; Nikitin, Frederic; Gluck, Florent; Lisacek, Frederique; Scherl, Alexander; Muller, Markus

    2013-12-01

    Data-independent mass spectrometry activates all ion species isolated within a given mass-to-charge window ( m/z) regardless of their abundance. This acquisition strategy overcomes the traditional data-dependent ion selection boosting data reproducibility and sensitivity. However, several tandem mass (MS/MS) spectra of the same precursor ion are acquired during chromatographic elution resulting in large data redundancy. Also, the significant number of chimeric spectra and the absence of accurate precursor ion masses hamper peptide identification. Here, we describe an algorithm to preprocess data-independent MS/MS spectra by filtering out noise peaks and clustering the spectra according to both the chromatographic elution profiles and the spectral similarity. In addition, we developed an approach to estimate the m/z value of precursor ions from clustered MS/MS spectra in order to improve database search performance. Data acquired using a small 3 m/z units precursor mass window and multiple injections to cover a m/z range of 400-1400 was processed with our algorithm. It showed an improvement in the number of both peptide and protein identifications by 8 % while reducing the number of submitted spectra by 18 % and the number of peaks by 55 %. We conclude that our clustering method is a valid approach for data analysis of these data-independent fragmentation spectra. The software including the source code is available for the scientific community.

  2. Mass Spectra of Individual Aerosol Particles Acquired During Intercepts of a Space Shuttle Exhaust Plume

    NASA Astrophysics Data System (ADS)

    Cziczo, D. J.; Cziczo, D. J.; Murphy, D. M.; Thomson, D. S.; Thomson, D. S.

    2001-12-01

    The WB-57 aircraft accomplished fourteen distinct stratospheric intercepts of the exhaust plume from a space shuttle during ACCENT 2000. Liftoff of the shuttle Atlantis for STS-106 occurred at 8:46 am local (12:46 UTC) with intercepts occurring from 5 to 90 minutes afterward. The Particle Analysis by Laser Mass Spectrometry (PALMS) instrument, mounted in the nose of the aircraft, was used to acquire individual mass spectra of over 2500 particles during these intercepts. The majority of positive mass spectra indicate the presence of the metals Al, Fe, Zn, Ga, and V, all components found in the solid rocket fuel. Organic material, presumably from binding and curing agents, was also present. Negative mass spectra showed Cl from the oxidizer, ammonium perchlorate, as well as water. Rare exotic particles, for example those containing Ti and Ag and possibly formed during engine or seal ablation, were also detected. Particles originating from shuttle exhaust but also containing significant sulfuric acid were common toward the outer edge of the plume, especially during late encounters, suggesting that deposition or aerosol collision had occurred.

  3. AN ION CORRELATION PROGRAM FOR DECONVOLUTING COMPOSITE MASS SPECTRA ACQUIRED USING A DIRECT SURFACE IONIZATION SOURCE INTERFACED TO A TIME-OF-FLIGHT MASS SPECTROMETER

    EPA Science Inventory

    The rapid sampling provided by the DART in ambient air will allow rapid delineation of areas of dispersed chemicals after natural or man-made disasters. Exact masses and RIAs of dimer, precursor, and product ions measured by the oa-TOFMS entered dinto the Ion Correlation Program...

  4. Error Analysis of Remotely-Acquired Mossbauer Spectra

    NASA Technical Reports Server (NTRS)

    Schaefer, Martha W.; Dyar, M. Darby; Agresti, David G.; Schaefer, Bradley E.

    2005-01-01

    On the Mars Exploration Rovers, Mossbauer spectroscopy has recently been called upon to assist in the task of mineral identification, a job for which it is rarely used in terrestrial studies. For example, Mossbauer data were used to support the presence of olivine in Martian soil at Gusev and jarosite in the outcrop at Meridiani. The strength (and uniqueness) of these interpretations lies in the assumption that peak positions can be determined with high degrees of both accuracy and precision. We summarize here what we believe to be the major sources of error associated with peak positions in remotely-acquired spectra, and speculate on their magnitudes. Our discussion here is largely qualitative because necessary background information on MER calibration sources, geometries, etc., have not yet been released to the PDS; we anticipate that a more quantitative discussion can be presented by March 2005.

  5. PIA update: Correlation analyses of mass spectra

    NASA Technical Reports Server (NTRS)

    Mason, L. W.; Clark, B. C.

    1988-01-01

    The PIA instrument aboard the Giotto spacecraft (a time of flight spectrometer) has been presented elsewhere. The mass spectra used in this analysis were decoded and mass numbers assigned according to the presence of carbon and silver, using the global values for these elements in their spectral absence. The results presented here were obtained using a frequency of occurrence based on analysis which correlated how often mass numbers appear in the mass spectra and which mass numbers tend to occur together in the same spectra; no amplitude information is utilized. The data are presented as plots of mass vs coincident mass for different subsets of the PIA data set, with both axes having units of atomic mass. Frequency contours are plotted at approximately five percent contour intervals, relative to the maximum AMU occurrence in that plot. The plots presented are symmetrical about the matrix diagonal, i.e., every mass is coincident with itself in a given spectra.

  6. Reduction of multielement mass spectra

    SciTech Connect

    Russ, G.P. III; Caffee, M.W.; Hudson, G.B.; Storch, N.A.

    1990-06-29

    Even though the spectra obtained by inductively coupled plasma source spectrometry (ICP-MS) are relatively simple, their interpretation can be complicated by the presence of molecular and isobaric interferants. To the extent that isotopic abundances are known and constant, one can treat observed spectra as sums of known components. A linear decomposition approach for determining the concentrations of the components in a spectrum and correctly propagating uncertainties is presented. This technique differs from linear regression in that an exact fit is made to a subset of isotopes and goodness-of-fit is evaluated from the deviations between the predicted and measured intensities of the other, unfit isotopes. This technique can be applied to a wide range of spectral fitting problems. In this paper, its applicability to ICP-MS spectra is used to demonstrate the use and utility of the technique. 2 refs., 9 figs.

  7. Processing and classification of protein mass spectra.

    PubMed

    Hilario, Melanie; Kalousis, Alexandros; Pellegrini, Christian; Müller, Markus

    2006-01-01

    Among the many applications of mass spectrometry, biomarker pattern discovery from protein mass spectra has aroused considerable interest in the past few years. While research efforts have raised hopes of early and less invasive diagnosis, they have also brought to light the many issues to be tackled before mass-spectra-based proteomic patterns become routine clinical tools. Known issues cover the entire pipeline leading from sample collection through mass spectrometry analytics to biomarker pattern extraction, validation, and interpretation. This study focuses on the data-analytical phase, which takes as input mass spectra of biological specimens and discovers patterns of peak masses and intensities that discriminate between different pathological states. We survey current work and investigate computational issues concerning the different stages of the knowledge discovery process: exploratory analysis, quality control, and diverse transforms of mass spectra, followed by further dimensionality reduction, classification, and model evaluation. We conclude after a brief discussion of the critical biomedical task of analyzing discovered discriminatory patterns to identify their component proteins as well as interpret and validate their biological implications.

  8. Handbook of mass spectra of environmental contaminants

    SciTech Connect

    Hites, R.A.

    1985-01-01

    This handbook is a collection of the electron impact mass spectra of 394 commonly encountered environmental pollutants. Each page is devoted to the examination of a single pollutant, which is presented as a bar graph always starting at M/z = 40. Each spectra is determined by analyses of data in EPA data bases. The major fragment ions are correlated with their respective structure. The mass and intensity of the four most intense ions in the spectrum are given. Each spectrum is marked to indicate the origin of the selected fragment ions. For each spectra, also given are the approved name of the chemical Abstract Service, the common name of the compound, the article number (if any) given to the Merck Index, the CAS Registry Number, the molecular formula, and the nominal molecular weight of the compound. Each spectra is indexed by common chemical name, CAS Registry Number, exact molecular weight, and intense peaks.

  9. Reanalysis of Tyrannosaurus rex Mass Spectra.

    PubMed

    Bern, Marshall; Phinney, Brett S; Goldberg, David

    2009-09-01

    Asara et al. reported the detection of collagen peptides in a 68-million-year-old Tyrannosaurus rex bone by shotgun proteomics. This finding has been called into question as a possible statistical artifact. We reanalyze Asara et al.'s tandem mass spectra using a different search engine and different statistical tools. Our reanalysis shows a sample containing common laboratory contaminants, soil bacteria, and bird-like hemoglobin and collagen.

  10. Method and system for calibrating acquired spectra for use in spectral analysis

    DOEpatents

    Reber, Edward L.; Rohde, Kenneth W.; Blackwood, Larry G.

    2010-09-14

    A method for calibrating acquired spectra for use in spectral analysis includes performing Gaussian peak fitting to spectra acquired by a plurality of NaI detectors to define peak regions. A Na and annihilation doublet may be located among the peak regions. A predetermined energy level may be applied to one of the peaks in the doublet and a location of a hydrogen peak may be predicted based on the location of at least one of the peaks of the doublet. Control systems for calibrating spectra are also disclosed.

  11. Odor Impression Prediction from Mass Spectra.

    PubMed

    Nozaki, Yuji; Nakamoto, Takamichi

    2016-01-01

    The sense of smell arises from the perception of odors from chemicals. However, the relationship between the impression of odor and the numerous physicochemical parameters has yet to be understood owing to its complexity. As such, there is no established general method for predicting the impression of odor of a chemical only from its physicochemical properties. In this study, we designed a novel predictive model based on an artificial neural network with a deep structure for predicting odor impression utilizing the mass spectra of chemicals, and we conducted a series of computational analyses to evaluate its performance. Feature vectors extracted from the original high-dimensional space using two autoencoders equipped with both input and output layers in the model are used to build a mapping function from the feature space of mass spectra to the feature space of sensory data. The results of predictions obtained by the proposed new method have notable accuracy (R≅0.76) in comparison with a conventional method (R≅0.61). PMID:27326765

  12. Odor Impression Prediction from Mass Spectra

    PubMed Central

    Nakamoto, Takamichi

    2016-01-01

    The sense of smell arises from the perception of odors from chemicals. However, the relationship between the impression of odor and the numerous physicochemical parameters has yet to be understood owing to its complexity. As such, there is no established general method for predicting the impression of odor of a chemical only from its physicochemical properties. In this study, we designed a novel predictive model based on an artificial neural network with a deep structure for predicting odor impression utilizing the mass spectra of chemicals, and we conducted a series of computational analyses to evaluate its performance. Feature vectors extracted from the original high-dimensional space using two autoencoders equipped with both input and output layers in the model are used to build a mapping function from the feature space of mass spectra to the feature space of sensory data. The results of predictions obtained by the proposed new method have notable accuracy (R≅0.76) in comparison with a conventional method (R≅0.61). PMID:27326765

  13. Peptide identification by database search of mixture tandem mass spectra.

    PubMed

    Wang, Jian; Bourne, Philip E; Bandeira, Nuno

    2011-12-01

    In high-throughput proteomics the development of computational methods and novel experimental strategies often rely on each other. In certain areas, mass spectrometry methods for data acquisition are ahead of computational methods to interpret the resulting tandem mass spectra. Particularly, although there are numerous situations in which a mixture tandem mass spectrum can contain fragment ions from two or more peptides, nearly all database search tools still make the assumption that each tandem mass spectrum comes from one peptide. Common examples include mixture spectra from co-eluting peptides in complex samples, spectra generated from data-independent acquisition methods, and spectra from peptides with complex post-translational modifications. We propose a new database search tool (MixDB) that is able to identify mixture tandem mass spectra from more than one peptide. We show that peptides can be reliably identified with up to 95% accuracy from mixture spectra while considering only a 0.01% of all possible peptide pairs (four orders of magnitude speedup). Comparison with current database search methods indicates that our approach has better or comparable sensitivity and precision at identifying single-peptide spectra while simultaneously being able to identify 38% more peptides from mixture spectra at significantly higher precision.

  14. Analysis of low resolution mass spectra

    NASA Technical Reports Server (NTRS)

    Babst, R. W.; Shapiro, H.

    1971-01-01

    Computer program determines gas constituents from measurements of mass/peak-height spectrum from residual gas analyzer. Applications of program include residual gas analysis for work in space environmental simulators, space environment contamination, and air pollution monitoring.

  15. High-Resolution Analysis of Atmospheric Mass Spectra: Identification, Resolution, Assignment of complex mass spectra

    NASA Astrophysics Data System (ADS)

    Stark, H.; Yatavelli, R. L. N.; Thompson, S.; Mazzoleni, L. R.; Kimmel, J.; Cubison, M.; Day, D. A.; Campuzano Jost, P.; Palm, B. B.; Chhabra, P. S.; Canagaratna, M. R.; Jayne, J. T.; Worsnop, D. R.; Jimenez, J. L.

    2015-12-01

    The troposphere can contain thousands of organic molecules with widely varying carbon numbers and levels of oxidation. Unraveling this complex molecular mixture gives new insights into key processes such as atmospheric processing, secondary aerosol formation, radiative properties as well as implications for human health. High-resolution time-of-flight chemical ionization mass spectrometry (HRToF-CIMS) is a powerful technique with the potential to provide many insights into this complex mix of molecules. We have developed new data analysis techniques to identify the most likely ions present in complex mass spectra in which individual peaks strongly overlap. New ancillary algorithms will also be presented to first develop a list of all possible formulas for this particular ion chemistry and then to automatically assign possible ions to the likely peak positions. Spectral simulation experiments confirm that bulk elemental properties such as oxidation state and carbon number can be reliably extracted from this method. Comparison of results from a CIMS operated during the 2011 BEACHON-RoMBAS campaign in the Colorado Rocky Mountains to electrospray-ultra-high-resolution mass spectrometry data from compounds measured in another forest in the Rockies allows a comparison of the compounds and compound classes measured by both techniques. We will also address the problem of quantifying ion signals from the organic molecule mix encountered in this study by a new method to calculate approximate sensitivities for acetate ionization chemistry to help quantifying concentrations of atmospheric compounds. We applied the above methods to a dataset from the micro-orifice volatilization impactor (MOVI)-CIMS collected during August 2011 as part of the BEACHON campaign. Calculated atmospheric bulk elemental parameters such as diurnal cycles of carbon number and oxidation state from both gas phase and aerosols from a pine forest environment will be presented and compared to data from

  16. Reflectance calibration and shadow effect of VNIS spectra acquired by the Yutu rover

    NASA Astrophysics Data System (ADS)

    Hu, Sen; Lin, Yang-Ting; Liu, Bin; Yang, Wei; He, Zhi-Ping; Xing, Wei-Fan

    2015-09-01

    Yutu is the first lunar rover after the Apollo program and Luna missions. One of the payloads on the Yutu rover, the Visible and Near-infrared Imaging Spectrometer (VNIS), has acquired four VIS/NIR images and SWIR spectra near its landing site in Mare Imbrium. The radiance images were reduced through repairing bad lines and bad points, and applying flat field correction, and then were converted into reflectance values based on the solar irradiance and angles of incidence. A significant shadow effect was observed in the VIS/NIR image. The shadowed regions show lower reflectance with a darkening trend compared with illuminated regions. The reflectance increased by up to 24% for entire images and 17% for the VIS/NIR-SWIR overlapping regions after shadow correction. The correction for the shadow effect will remarkably decrease the estimate of FeO content, by up to 4.9 wt.% in this study. The derived FeO contents of CD-005∼008 after shadow correction are around 18.0 wt.%.

  17. Active and sterile neutrino mass effects on beta decay spectra

    SciTech Connect

    Boillos, Juan Manuel; Moya de Guerra, Elvira

    2013-06-10

    We study the spectra of the emitted charged leptons in charge current weak nuclear processes to analyze the effect of neutrino masses. Standard active neutrinos are studied here, with masses of the order of 1 eV or lower, as well as sterile neutrinos with masses of a few keV. The latter are warm dark matter (WDM) candidates hypothetically produced or captured as small mixtures with the active neutrinos. We compute differential decay or capture rates spectra in weak charged processes of different nuclei ({sup 3}H, {sup 187}Re, {sup 107}Pd, {sup 163}Ho, etc) using different masses of both active and sterile neutrinos and different values of the mixing parameter.

  18. Mass Spectra and Ion Collision Cross Sections of Hemoglobin

    NASA Astrophysics Data System (ADS)

    Kang, Yang; Terrier, Peran; Douglas, D. J.

    2011-02-01

    Mass spectra of commercially obtained hemoglobin (Hb) show higher levels of monomer and dimer ions, heme-deficient dimer ions, and apo-monomer ions than hemoglobin freshly prepared from blood. This has previously been attributed to oxidation of commercial Hb. Further, it has been reported that that dimer ions from commercial bovine Hb have lower collision cross sections than low charge state monomer ions. To investigate these effects further, we have recorded mass spectra of fresh human Hb, commercial human and bovine Hb, fresh human Hb oxidized with H2O2, lyophilized fresh human Hb, fresh human Hb both lyophilized and chemically oxidized, and commercial human Hb oxidized with H2O2. Masses of α-monomer ions of all hemoglobins agree with the masses expected from the sequences within 3 Da or better. Mass spectra of the β chains of commercial Hb and oxidized fresh human Hb show a peak or shoulder on the high mass side, consistent with oxidation of the protein. Both commercial proteins and oxidized fresh human Hb produce heme-deficient dimers with masses 32 Da greater than expected and higher levels of monomer and dimer ions than fresh Hb. Lyophilization or oxidation of Hb both produce higher levels of monomer and dimer ions in mass spectra. Fresh human Hb, commercial human Hb, commercial bovine Hb, and oxidized commercial human Hb all give dimer ions with cross sections greater than monomer ions. Thus, neither oxidation of Hb or the difference in sequence between human and bovine Hb make substantial differences to cross sections of ions.

  19. Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra

    PubMed Central

    Diament, Benjamin; Noble, William Stafford

    2011-01-01

    Computational analysis of mass spectra remains the bottleneck in many proteomics experiments. SEQUEST was one of the earliest software packages to identify peptides from mass spectra by searching a database of known peptides. Though still popular, SEQUEST performs slowly. Crux and TurboSEQUEST have successfully sped up SEQUEST by adding a precomputed index to the search, but the demand for ever-faster peptide identification software continues to grow. Tide, introduced here, is a software program that implements the SEQUEST algorithm for peptide identification and that achieves a dramatic speedup over Crux and SEQUEST. The optimization strategies detailed here employ a combination of algorithmic and software engineering techniques to achieve speeds up to 170 times faster than a recent version of SEQUEST that uses indexing. For example, on a single Xeon CPU, Tide searches 10,000 spectra against a tryptic database of 27,499 C. elegans proteins at a rate of 1,550 spectra per second, which compares favorably with a rate of 8.8 spectra per second for a recent version of SEQUEST with index running on the same hardware. PMID:21761931

  20. Mass spectra of 0+-, 1-+, and 2+- exotic glueballs

    NASA Astrophysics Data System (ADS)

    Tang, Liang; Qiao, Cong-Feng

    2016-03-01

    With appropriate interpolating currents the mass spectra of 0+-, 1-+, and 2+- oddballs are studied in the framework of QCD sum rules (QCDSR). We find there exits one stable 0+- oddball with mass of 4.57 ± 0.13GeV, and one stable 2+- oddball with mass of 6.06 ± 0.13GeV, whereas, no stable 1-+ oddball shows up. The possible production and decay modes of these glueballs with unconventional quantum numbers are analyzed, which are hopefully measurable in either BELLEII, PANDA, Super-B or LHCb experiments.

  1. Label-free peptide profiling of Orbitrap™ full mass spectra

    PubMed Central

    2011-01-01

    Background We developed a new version of the open source software package Peptrix that can yet compare large numbers of Orbitrap™ LC-MS data. The peptide profiling results for Peptrix on MS1 spectra were compared with those obtained from a small selection of open source and commercial software packages: msInspect, Sieve™ and Progenesis™. The properties compared in these packages were speed, total number of detected masses, redundancy of masses, reproducibility in numbers and CV of intensity, overlap of masses, and differences in peptide peak intensities. Reproducibility measurements were taken for the different MS1 software applications by measuring in triplicate a complex peptide mixture of immunoglobulin on the Orbitrap™ mass spectrometer. Values of peptide masses detected from the high intensity peaks of the MS1 spectra by peptide profiling were verified with values of the MS2 fragmented and sequenced masses that resulted in protein identifications with a significant score. Findings Peptrix finds about the same number of peptide features as the other packages, but peptide masses are in some cases approximately 5 to 10 times less redundant present in the peptide profile matrix. The Peptrix profile matrix displays the largest overlap when comparing the number of masses in a pair between two software applications. The overlap of peptide masses between software packages of low intensity peaks in the spectra is remarkably low with about 50% of the detected masses in the individual packages. Peptrix does not differ from the other packages in detecting 96% of the masses that relate to highly abundant sequenced proteins. MS1 peak intensities vary between the applications in a non linear way as they are not processed using the same method. Conclusions Peptrix is capable of peptide profiling using Orbitrap™ files and finding differential expressed peptides in body fluid and tissue samples. The number of peptide masses detected in Orbitrap™ files can be

  2. Higher-order mass defect analysis for mass spectra of complex organic mixtures.

    PubMed

    Roach, Patrick J; Laskin, Julia; Laskin, Alexander

    2011-06-15

    Higher-order mass defect analysis is introduced as a unique formula assignment and visualization method for the analysis of complex mass spectra. This approach is an extension of the concepts of Kendrick mass transformation widely used for identification of homologous compounds differing only by a number of base units (e.g., CH(2), H(2), O, CH(2)O, etc.) in complex mixtures. We present an iterative renormalization routine for defining higher-order homologous series and multidimensional clustering of mass spectral features. This approach greatly simplifies visualization of complex mass spectra and increases the number of chemical formulas that can be confidently assigned for given mass accuracy. The potential for using higher-order mass defects for data reduction and visualization is shown. Higher-order mass defect analysis is described and demonstrated through third-order analysis of a deisotoped high-resolution mass spectrum of crude oil containing nearly 13,000 peaks. PMID:21526851

  3. Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments

    NASA Astrophysics Data System (ADS)

    Bazsó, Fanni Laura; Ozohanics, Oliver; Schlosser, Gitta; Ludányi, Krisztina; Vékey, Károly; Drahos, László

    2016-08-01

    The similarity between two tandem mass spectra, which were measured on different instruments, was compared quantitatively using the similarity index (SI), defined as the dot product of the square root of peak intensities in the respective spectra. This function was found to be useful for comparing energy-dependent tandem mass spectra obtained on various instruments. Spectral comparisons show the similarity index in a 2D "heat map", indicating which collision energy combinations result in similar spectra, and how good this agreement is. The results and methodology can be used in the pharma industry to design experiments and equipment well suited for good reproducibility. We suggest that to get good long-term reproducibility, it is best to adjust the collision energy to yield a spectrum very similar to a reference spectrum. It is likely to yield better results than using the same tuning file, which, for example, does not take into account that contamination of the ion source due to extended use may influence instrument tuning. The methodology may be used to characterize energy dependence on various instrument types, to optimize instrumentation, and to study the influence or correlation between various experimental parameters.

  4. Theory analysis of mass spectra of long-chain isocyanates.

    PubMed

    Liu, Dongliang; Hao, Ce; Zhang, Hua; Qiao, Weihong; Li, Zongshi; Yu, Guanghui; Yan, Kelu; Guo, Yuliang; Cheng, Lvbo

    2008-07-01

    Electron impact mass spectra of four long-chain isocyanates, lauryl isocyanate, tetradecyl isocyanate, hexadecyl isocyanate and octadecyl isocyanate, were obtained with a GCT high-resolution time-of-flight mass spectrometer. The four isocyanates studied gave a common base peak of m/z 99, which suggested the formation of a stable six-membered ring structure to decentralize the positive charge. Quantum-mechanical energy calculation justified that the six-membered ring base peak had the lowest energy. The positive charge assigned during the fragmentation of the radical cation, and the relative intensity of the fragment ion peaks, were explained by quantum-mechanical calculations as well.

  5. Systematization of the mass spectra for speciation of inorganic salts with static secondary ion mass spectrometry.

    PubMed

    Van Ham, Rita; Van Vaeck, Luc; Adams, Freddy C; Adriaens, Annemie

    2004-05-01

    The analytical use of mass spectra from static secondary ion mass spectrometry for the molecular identification of inorganic analytes in real life surface layers and microobjects requires an empirical insight in the signals to be expected from a given compound. A comprehensive database comprising over 50 salts has been assembled to complement prior data on oxides. The present study allows the systematic trends in the relationship between the detected signals and molecular composition of the analyte to be delineated. The mass spectra provide diagnostic information by means of atomic ions, structural fragments, molecular ions, and adduct ions of the analyte neutrals. The prediction of mass spectra from a given analyte must account for the charge state of the ions in the salt, the formation of oxide-type neutrals from oxy salts, and the occurrence of oxidation-reduction processes.

  6. Efficient Methods to Generate Reproducible Mass Spectra in Matrix-Assisted Laser Desorption Ionization of Peptides

    NASA Astrophysics Data System (ADS)

    Ahn, Sung Hee; Park, Kyung Man; Bae, Yong Jin; Kim, Myung Soo

    2013-06-01

    In our previous matrix-assisted laser desorption ionization (MALDI) studies of peptides, we found that their mass spectra were virtually determined by the effective temperature in the early matrix plume, Tearly, when samples were rather homogeneous. This empirical rule allowed acquisition of quantitatively reproducible spectra. A difficulty in utilizing this rule was the complicated spectral treatment needed to get Tearly. In this work, we found another empirical rule that the total number of particles hitting the detector, or TIC, was a good measure of the spectral temperature and, hence, selection of spectra with the same TIC resulted in reproducible spectra. We also succeeded in obtaining reproducible spectra throughout a measurement by controlling TIC near a preset value through feedback adjustment of laser pulse energy. Both TIC selection and TIC control substantially reduced the shot-to-shot spectral variation in a spot, spot-to-spot variation in a sample, and even sample-to-sample variation in MALDI using α-cyano-4-hydroxycinnamic acid or 2,5-dihydroxybenzoic acid as matrix. Based on the utilization of acquired data, TIC control was more efficient than TIC selection by an order of magnitude. Both techniques produced calibration curves with excellent linearity, suggesting their utility in quantification of peptides.

  7. The laser desorption/laser ionization mass spectra of some indole derivatives and alkaloids

    NASA Astrophysics Data System (ADS)

    Rogers, Kevin; Milnes, John; Gormally, John

    1992-06-01

    The laser desorption and laser ionization mass spectra of some indole derivatives and alkaloids are described with particular reference to their modes of fragmentation. Mass spectra of yohimbine, reserpine, quinine and quinidine are presented. Full experimental details are given.

  8. ClusterSculptor: Software for Expert-Steered Classification of Single Particle Mass Spectra

    SciTech Connect

    Zelenyuk, Alla; Imre, Dan G.; Nam, Eun Ju; Han, Yiping; Mueller, Klaus

    2008-08-01

    To take full advantage of the vast amount of highly detailed data acquired by single particle mass spectrometers requires that the data be organized according to some rules that have the potential to be insightful. Most commonly statistical tools are used to cluster the individual particle mass spectra on the basis of their similarity. Cluster analysis is a powerful strategy for the exploration of high-dimensional data in the absence of a-priori hypotheses or data classification models, and the results of cluster analysis can then be used to form such models. More often than not, when examining the data clustering results we find that many clusters contain particles of different types and that many particles of one type end up in a number of separate clusters. Our experience with cluster analysis shows that we have a vast amount of non-compiled knowledge and intuition that should be brought to bear in this effort. We will present new software we call ClusterSculptor that provides comprehensive and intuitive framework to aid scientists in data classification. ClusterSculptor uses k-means as the overall clustering engine, but allows tuning its parameters interactively, based on a non-distorted compact visual presentation of the inherent characteristics of the data in high-dimensional space. ClusterSculptor provides all the tools necessary for a high-dimensional activity we call cluster sculpting. ClusterSculptor is designed to be coupled to SpectraMiner, our data mining and visualization software package. The data are first visualized with SpectraMiner and identified problems are exported to ClusterSculptor, where the user steers the reclassification and recombination of clusters of tens of thousands particle mass spectra in real-time. The resulting sculpted clusters can be then imported back into SpectraMiner. Here we will greatly improved single particle chemical speciation in an example of application of this new tool to a number of particle types of atmospheric

  9. Machine learning approaches to lung cancer prediction from mass spectra.

    PubMed

    Hilario, Melanie; Kalousis, Alexandros; Müller, Markus; Pellegrini, Christian

    2003-09-01

    We addressed the problem of discriminating between 24 diseased and 17 healthy specimens on the basis of protein mass spectra. To prepare the data, we performed mass to charge ratio (m/z) normalization, baseline elimination, and conversion of absolute peak height measures to height ratios. After preprocessing, the major difficulty encountered was the extremely large number of variables (1676 m/z values) versus the number of examples (41). Dimensionality reduction was treated as an integral part of the classification process; variable selection was coupled with model construction in a single ten-fold cross-validation loop. We explored different experimental setups involving two peak height representations, two variable selection methods, and six induction algorithms, all on both the original 1676-mass data set and on a prescreened 124-mass data set. Highest predictive accuracies (1-2 off-sample misclassifications) were achieved by a multilayer perceptron and Naïve Bayes, with the latter displaying more consistent performance (hence greater reliability) over varying experimental conditions. We attempted to identify the most discriminant peaks (proteins) on the basis of scores assigned by the two variable selection methods and by neural network based sensitivity analysis. These three scoring schemes consistently ranked four peaks as the most relevant discriminators: 11683, 1403, 17350 and 66107.

  10. Comparison of Newly Acquired Lunar Spectra with the Titanium Abundance Maps Derived from Clementine

    NASA Technical Reports Server (NTRS)

    Holsclaw, G. M.; McClintock, W. E.; Robinson, M. S.

    2005-01-01

    The Mercury Atmospheric and Surface Composition Spectrometer (MASCS) is one of seven science instruments onboard NASA's MESSENGER mission, currently en-route to the planet Mercury. One of MASCS s components, referred to as the Visible and Near Infrared Spectrograph (VIRS), will record reflectance spectra of the surface in order to characterize the mineralogy of the planet [1]. The lunar highlands and the average mercurian crust are proposed to be compositionally similar [i.e. 2]. In preparation to interpret VIRS reflectance spectra of Mercury to be first obtained in 2008, the Moon has been observed with an engineering model of the VIRS from a ground-based telescope. In this study, the ultraviolet and visible region of the spectrum is compared with titanium content in the lunar regolith.

  11. Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides.

    PubMed

    Liu, Wei-Ting; Ng, Julio; Meluzzi, Dario; Bandeira, Nuno; Gutierrez, Marcelino; Simmons, Thomas L; Schultz, Andrew W; Linington, Roger G; Moore, Bradley S; Gerwick, William H; Pevzner, Pavel A; Dorrestein, Pieter C

    2009-06-01

    Natural and non-natural cyclic peptides are a crucial component in drug discovery programs because of their considerable pharmaceutical properties. Cyclosporin, microcystins, and nodularins are all notable pharmacologically important cyclic peptides. Because these biologically active peptides are often biosynthesized nonribosomally, they often contain nonstandard amino acids, thus increasing the complexity of the resulting tandem mass spectrometry data. In addition, because of the cyclic nature, the fragmentation patterns of many of these peptides showed much higher complexity when compared to related counterparts. Therefore, at the present time it is still difficult to annotate cyclic peptides MS/MS spectra. In this current work, an annotation program was developed for the annotation and characterization of tandem mass spectra obtained from cyclic peptides. This program, which we call MS-CPA is available as a web tool (http://lol.ucsd.edu/ms-cpa_v1/Input.py). Using this program, we have successfully annotated the sequence of representative cyclic peptides, such as seglitide, tyrothricin, desmethoxymajusculamide C, dudawalamide A, and cyclomarins, in a rapid manner and also were able to provide the first-pass structure evidence of a newly discovered natural product based on predicted sequence. This compound is not available in sufficient quantities for structural elucidation by other means such as NMR. In addition to the development of this cyclic annotation program, it was observed that some cyclic peptides fragmented in unexpected ways resulting in the scrambling of sequences. In summary, MS-CPA not only provides a platform for rapid confirmation and annotation of tandem mass spectrometry data obtained with cyclic peptides but also enables quantitative analysis of the ion intensities. This program facilitates cyclic peptide analysis, sequencing, and also acts as a useful tool to investigate the uncommon fragmentation phenomena of cyclic peptides and aids the

  12. Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by search engines?

    PubMed

    Chalkley, Robert J; Baker, Peter R; Hansen, Kirk C; Medzihradszky, Katalin F; Allen, Nadia P; Rexach, Michael; Burlingame, Alma L

    2005-08-01

    An in-depth analysis of a multidimensional chromatography-mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument was carried out. A total of 3269 CID spectra were acquired. Through manual verification of database search results and de novo interpretation of spectra 2368 spectra could be confidently determined as predicted tryptic peptides. A detailed analysis of the non-matching spectra was also carried out, highlighting what the non-matching spectra in a database search typically are composed of. The results of this comprehensive dataset study demonstrate that QqTOF instruments produce information-rich data of which a high percentage of the data is readily interpretable.

  13. De novo sequencing of peptides from top-down tandem mass spectra

    SciTech Connect

    Vyatkina, Kira; Wu, Si; Dekker, Leendert J.; vanDuijn, Martijn M.; Liu, Xiaowen; Tolic, Nikola; Dvorkin, Mikhail; Alexandrova, Sonya; Luider, Theo N.; Pasa-Tolic, Ljiljana; Pevzner, Pavel A.

    2015-09-28

    De novo sequencing of proteins and peptides is one of the most important problems in mass spectrometry-driven proteomics. A variety of methods have been developed to accomplish this task from a set of bottom-up tandem (MS/MS) mass spectra. However, a more recently emerged top-down technology, now gaining more and more popularity, opens new perspectives for protein analysis and characterization, implying a need in efficient algorithms for processing this kind of MS/MS data. Here we describe a method that allows to retrieve from a set of top-down MS/MS spectra long and accurate sequence fragments of the proteins contained in a sample. To this end, we outline a strategy for generating high-quality sequence tags from top-down spectra, and introduce the concept of a T-Bruijn graph by adapting to the case of tags the notion of an A-Bruijn graph widely used in genomics. The output of the proposed approach represents the set of amino acid strings spelled out by optimal paths in the connected components of a T-Bruijn graph. We illustrate its performance on top-down datasets acquired from carbonic anhydrase 2 (CAH2) and the Fab region of alemtuzumab.

  14. Visible and Near-IR Reflectance Spectra of Smectite Acquired Under Dry Conditions for Interpretation of Martian Surface Mineralogy

    NASA Technical Reports Server (NTRS)

    Morris, Richard V.; Achilles, Cherie N; Archer, Paul D.; Graff, Trevor G.; Agresti, David G.; Ming, Douglas W; Golden, Dadi C.; Mertzman, Stanley A.

    2011-01-01

    Visible and near-IR (VNIR) spectra from the MEx OMEGA and the MRO CRISM hyper-spectral imaging instruments have spectral features associated with the H2O molecule and M OH functional groups (M = Mg, Fe, Al, and Si). Mineralogical assignments of martian spectral features are made on the basis of laboratory VNIR spectra, which were often acquired under ambient (humid) conditions. Smectites like nontronite, saponite, and montmorillionite have interlayer H2O that is exchangeable with their environment, and we have acquired smectite reflectance spectra under dry environmental conditions for interpretation of martian surface mineralogy. We also obtained chemical, Moessbauer (MB), powder X-ray diffraction (XRD), and thermogravimetric (TG) data to understand variations in spectral properties. VNIR spectra were recorded in humid lab air at 25-35C, in a dynamic dry N2 atmosphere (50-150 ppmv H2O) after exposing the smectite samples (5 nontronites, 3 montmorillionites, and 1 saponite) to that atmosphere for up to approximately l000 hr each at 25-35C, approximately 105C, and approximately 215C, and after re-exposure to humid lab air. Heating at 105C and 215C for approximately 1000 hr is taken as a surrogate for geologic time scales at lower temperatures. Upon exposure to dry N2, the position and intensity of spectral features associated with M-OH were relatively insensitive to the dry environment, and the spectral features associated with H2O (e.g., approximately 1.90 micrometers) decreased in intensity and are sometimes not detectable by the end of the 215C heating step. The position and intensity of H2O spectral features recovered upon re-exposure to lab air. XRD data show interlayer collapse for the nontronites and Namontmorillionites, with the interlayer remaining collapsed for the latter after re-exposure to lab air. The interlayer did not collapse for the saponite and Ca-montmorillionite. TG data show that the concentration of H2O derived from structural OH was invariant

  15. Charmed-strange mesons revisited: Mass spectra and strong decays

    NASA Astrophysics Data System (ADS)

    Song, Qin-Tao; Chen, Dian-Yong; Liu, Xiang; Matsuki, Takayuki

    2015-03-01

    Inspired by the present experimental status of charmed-strange mesons, we perform a systematic study of the charmed-strange meson family in which we calculate the mass spectra of the charmed-strange meson family by taking a screening effect into account in the Godfrey-Isgur model and investigate the corresponding strong decays via the quark pair creation model. These phenomenological analyses of charmed-strange mesons not only shed light on the features of the observed charmed-strange states, but also provide important information on future experimental search for the missing higher radial and orbital excitations in the charmed-strange meson family, which will be a valuable task in LHCb, the forthcoming Belle II, and PANDA.

  16. Electron-impact mass spectra of carbomethoxyl derivatives of cyclopropylthiophenes

    SciTech Connect

    Kadentsev, V.I.; Kolotyrkina, N.G.; Chizhov, O.S.; Shostakovskii, V.M.; Vasil'vitskii, A.A.; Zlatkina, V.L.

    1987-01-10

    In the mass spectra of carbomethoxyl derivatives of cyclopropylthiophene, intense ion peaks are observed, corresponding to successive elimination of MeO and COOMe radicals and the neutral fragments MeOH, HCOOMe, and CO from M/sup +./, so that the number of carbomethoxyl substituents in CPR can be determined. Mono- and gem-dicarbomethoxyl derivatives of cyclopropylthiophenes are characterized by rearrangements of M/sup +./ with migration of the MeO groups to the carbon atom adjacent to the thiophene ring. The presence of a methyl substituent at this carbon atom hinders this rearrangement. For the monocarbomethoxyl derivatives of cyclopropylthiophenes under electron impact, a splitting off of the methyl substituent of the ester groups is observed.

  17. Radiation anomaly detection algorithms for field-acquired gamma energy spectra

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Sanjoy; Maurer, Richard; Wolff, Ron; Guss, Paul; Mitchell, Stephen

    2015-08-01

    The Remote Sensing Laboratory (RSL) is developing a tactical, networked radiation detection system that will be agile, reconfigurable, and capable of rapid threat assessment with high degree of fidelity and certainty. Our design is driven by the needs of users such as law enforcement personnel who must make decisions by evaluating threat signatures in urban settings. The most efficient tool available to identify the nature of the threat object is real-time gamma spectroscopic analysis, as it is fast and has a very low probability of producing false positive alarm conditions. Urban radiological searches are inherently challenged by the rapid and large spatial variation of background gamma radiation, the presence of benign radioactive materials in terms of the normally occurring radioactive materials (NORM), and shielded and/or masked threat sources. Multiple spectral anomaly detection algorithms have been developed by national laboratories and commercial vendors. For example, the Gamma Detector Response and Analysis Software (GADRAS) a one-dimensional deterministic radiation transport software capable of calculating gamma ray spectra using physics-based detector response functions was developed at Sandia National Laboratories. The nuisance-rejection spectral comparison ratio anomaly detection algorithm (or NSCRAD), developed at Pacific Northwest National Laboratory, uses spectral comparison ratios to detect deviation from benign medical and NORM radiation source and can work in spite of strong presence of NORM and or medical sources. RSL has developed its own wavelet-based gamma energy spectral anomaly detection algorithm called WAVRAD. Test results and relative merits of these different algorithms will be discussed and demonstrated.

  18. Reactions and mass spectra of complex particles using Aerosol CIMS

    NASA Astrophysics Data System (ADS)

    Hearn, John D.; Smith, Geoffrey D.

    2006-12-01

    Aerosol chemical ionization mass spectrometry (CIMS) is used both on- and off-line for the analysis of complex laboratory-generated and ambient particles. One of the primary advantages of Aerosol CIMS is the low degree of ion fragmentation, making this technique well suited for investigating the reactivity of complex particles. To demonstrate the usefulness of this "soft" ionization, particles generated from meat cooking were reacted with ozone and the composition was monitored as a function of reaction time. Two distinct kinetic regimes were observed with most of the oleic acid in these particles reacting quickly but with 30% appearing to be trapped in the complex mixture. Additionally, detection limits are measured to be sufficiently low (100-200 ng/m3) to detect some of the more abundant constituents in ambient particles, including sulfate, which is measured in real-time at 1.2 [mu]g/m3. To better characterize complex aerosols from a variety of sources, a novel off-line collection method was also developed in which non-volatile and semi-volatile organics are desorbed from particles and concentrated in a cold U-tube. Desorption from the U-tube followed by analysis with Aerosol CIMS revealed significant amounts of nicotine in cigarette smoke and levoglucosan in oak and pine smoke, suggesting that this may be a useful technique for monitoring particle tracer species. Additionally, secondary organic aerosol formed from the reaction of ozone with R-limonene and volatile organics from orange peel were analyzed off-line showing large molecular weight products (m/z > 300 amu) that may indicate the formation of oligomers. Finally, mass spectra of ambient aerosol collected offline reveal a complex mixture of what appears to be highly processed organics, some of which may contain nitrogen.

  19. Game-theory-based search engine to automate the mass assignment in complex native electrospray mass spectra.

    PubMed

    Tseng, Yao-Hsin; Uetrecht, Charlotte; Yang, Shih-Chieh; Barendregt, Arjan; Heck, Albert J R; Peng, Wen-Ping

    2013-12-01

    Electrospray ionization coupled to native mass spectrometry (MS) has evolved into an important tool in structural biology to decipher the composition of protein complexes. However, the mass analysis of heterogeneous protein assemblies is hampered because of their overlapping charge state distributions, fine structure, and peak broadening. To facilitate the mass analysis, it is of importance to automate preprocessing raw mass spectra, assigning ion series to peaks and deciphering the subunit compositions. So far, the automation of preprocessing raw mass spectra has not been accomplished; Massign was introduced to simplify data analysis and decipher the subunit compositions. In this study, we develop a search engine, AutoMass, to automatically assign ion series to peaks without any additional user input, for example, limited ranges of charge states or ion mass. AutoMass includes an ion intensity-dependent method to check for Gaussian distributions of ion series and an ion intensity-independent method to address highly overlapping and non-Gaussian distributions. The minimax theorem from game theory is adopted to define the boundaries. With AutoMass, the boundaries of ion series in the well-resolved tandem mass spectra of the hepatitis B virus (HBV) capsids and those of the mass spectrum from CRISPR-related cascade protein complex are accurately assigned. Theoretical and experimental HBV ion masses are shown in agreement up to ~0.03%. The analysis is finished within a minute on a regular workstation. Moreover, less well-resolved mass spectra, for example, complicated multimer mass spectra and norovirus capsid mass spectra at different levels of desolvation, are analyzed. In sum, this first-ever fully automatic program reveals the boundaries of overlapping ion peak series and can further aid developing high-throughput native MS and top-down proteomics.

  20. Applying 'Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra' (SWATH) for systematic toxicological analysis with liquid chromatography-high-resolution tandem mass spectrometry.

    PubMed

    Arnhard, Kathrin; Gottschall, Anna; Pitterl, Florian; Oberacher, Herbert

    2015-01-01

    Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become an indispensable analytical technique in clinical and forensic toxicology for detection and identification of potentially toxic or harmful compounds. Particularly, non-target LC-MS/MS assays enable extensive and universal screening requested in systematic toxicological analysis. An integral part of the identification process is the generation of information-rich product ion spectra which can be searched against libraries of reference mass spectra. Usually, 'data-dependent acquisition' (DDA) strategies are applied for automated data acquisition. In this study, the 'data-independent acquisition' (DIA) method 'Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra' (SWATH) was combined with LC-MS/MS on a quadrupole-quadrupole-time-of-flight (QqTOF) instrument for acquiring informative high-resolution tandem mass spectra. SWATH performs data-independent fragmentation of all precursor ions entering the mass spectrometer in 21m/z isolation windows. The whole m/z range of interest is covered by continuous stepping of the isolation window. This allows numerous repeat analyses of each window during the elution of a single chromatographic peak and results in a complete fragment ion map of the sample. Compounds and samples typically encountered in forensic casework were used to assess performance characteristics of LC-MS/MS with SWATH. Our experiments clearly revealed that SWATH is a sensitive and specific identification technique. SWATH is capable of identifying more compounds at lower concentration levels than DDA does. The dynamic range of SWATH was estimated to be three orders of magnitude. Furthermore, the >600,000 SWATH spectra matched led to only 408 incorrect calls (false positive rate = 0.06 %). Deconvolution of generated ion maps was found to be essential for unravelling the full identification power of LC-MS/MS with SWATH. With the available software, however, only semi

  1. Automated Glycan Sequencing from Tandem Mass Spectra of N-Linked Glycopeptides.

    PubMed

    Yu, Chuan-Yih; Mayampurath, Anoop; Zhu, Rui; Zacharias, Lauren; Song, Ehwang; Wang, Lei; Mechref, Yehia; Tang, Haixu

    2016-06-01

    Mass spectrometry has become a routine experimental tool for proteomic biomarker analysis of human blood samples, partly due to the large availability of informatics tools. As one of the most common protein post-translational modifications (PTMs) in mammals, protein glycosylation has been observed to alter in multiple human diseases and thus may potentially be candidate markers of disease progression. While mass spectrometry instrumentation has seen advancements in capabilities, discovering glycosylation-related markers using existing software is currently not straightforward. Complete characterization of protein glycosylation requires the identification of intact glycopeptides in samples, including identification of the modification site as well as the structure of the attached glycans. In this paper, we present GlycoSeq, an open-source software tool that implements a heuristic iterated glycan sequencing algorithm coupled with prior knowledge for automated elucidation of the glycan structure within a glycopeptide from its collision-induced dissociation tandem mass spectrum. GlycoSeq employs rules of glycosidic linkage as defined by glycan synthetic pathways to eliminate improbable glycan structures and build reasonable glycan trees. We tested the tool on two sets of tandem mass spectra of N-linked glycopeptides cell lines acquired from breast cancer patients. After employing enzymatic specificity within the N-linked glycan synthetic pathway, the sequencing results of GlycoSeq were highly consistent with the manually curated glycan structures. Hence, GlycoSeq is ready to be used for the characterization of glycan structures in glycopeptides from MS/MS analysis. GlycoSeq is released as open source software at https://github.com/chpaul/GlycoSeq/ . PMID:27111718

  2. The electron impact mass spectra of di- and trinitrofluoranthenes.

    PubMed

    Ramdahl, T; Zielinska, B; Arey, J; Kondrat, R W

    1988-07-01

    The fragmentation pathways of a series of 18 dinitrofluoranthenes (DNF) and four trinitrofluoranthenes have been studied under electron impact conditions. In general, multiple losses of NO2, NO and CO from the molecular ion were observed. Quinonoid ions were observed in the spectra of DNF containing conjugated nitro groups. In addition, some unique fragmentation pathways were detected in the ortho-substituted 1,2- and 2,3-DNF and in the peri-substituted 3,4-DNF.

  3. New FORTRAN computer programs to acquire and process isotopic mass spectrometric data: Operator`s manual

    SciTech Connect

    Smith, D.H.; McKown, H.S.

    1993-09-01

    This TM is one of a pair that describes ORNL-developed software for acquisition and processing of isotope ratio mass spectral data. This TM is directed at the laboratory analyst. No technical knowledge of the programs and programming is required. It describes how to create and edit files, how to acquire and process data, and how to set up files to obtain the desired results. The aim of this TM is to serve as a utilitarian instruction manual, a {open_quotes}how to{close_quotes} approach rather than a {open_quotes}why?{close_quotes}

  4. Purification of pharmaceutical preparations using thin-layer chromatography to obtain mass spectra with Direct Analysis in Real Time and accurate mass spectrometry.

    PubMed

    Wood, Jessica L; Steiner, Robert R

    2011-06-01

    Forensic analysis of pharmaceutical preparations requires a comparative analysis with a standard of the suspected drug in order to identify the active ingredient. Purchasing analytical standards can be expensive or unattainable from the drug manufacturers. Direct Analysis in Real Time (DART™) is a novel, ambient ionization technique, typically coupled with a JEOL AccuTOF™ (accurate mass) mass spectrometer. While a fast and easy technique to perform, a drawback of using DART™ is the lack of component separation of mixtures prior to ionization. Various in-house pharmaceutical preparations were purified using thin-layer chromatography (TLC) and mass spectra were subsequently obtained using the AccuTOF™- DART™ technique. Utilizing TLC prior to sample introduction provides a simple, low-cost solution to acquiring mass spectra of the purified preparation. Each spectrum was compared against an in-house molecular formula list to confirm the accurate mass elemental compositions. Spectra of purified ingredients of known pharmaceuticals were added to an in-house library for use as comparators for casework samples. Resolving isomers from one another can be accomplished using collision-induced dissociation after ionization. Challenges arose when the pharmaceutical preparation required an optimized TLC solvent to achieve proper separation and purity of the standard. Purified spectra were obtained for 91 preparations and included in an in-house drug standard library. Primary standards would only need to be purchased when pharmaceutical preparations not previously encountered are submitted for comparative analysis. TLC prior to DART™ analysis demonstrates a time efficient and cost saving technique for the forensic drug analysis community. Copyright © 2011 John Wiley & Sons, Ltd.

  5. De Novo Correction of Mass Measurement Error in Low Resolution Tandem MS Spectra for Shotgun Proteomics

    NASA Astrophysics Data System (ADS)

    Egertson, Jarrett D.; Eng, Jimmy K.; Bereman, Michael S.; Hsieh, Edward J.; Merrihew, Gennifer E.; MacCoss, Michael J.

    2012-12-01

    We report an algorithm designed for the calibration of low resolution peptide mass spectra. Our algorithm is implemented in a program called FineTune, which corrects systematic mass measurement error in 1 min, with no input required besides the mass spectra themselves. The mass measurement accuracy for a set of spectra collected on an LTQ-Velos improved 20-fold from -0.1776 ± 0.0010 m/z to 0.0078 ± 0.0006 m/z after calibration (avg ± 95 % confidence interval). The precision in mass measurement was improved due to the correction of non-linear variation in mass measurement accuracy across the m/z range.

  6. First principles calculation of electron ionization mass spectra for selected organic drug molecules.

    PubMed

    Bauer, Christoph Alexander; Grimme, Stefan

    2014-11-21

    This study presents a showcase for the novel Quantum Chemistry Electron Ionization Mass Spectrometry (QCEIMS) method on five FDA-approved drugs. The method allows a first-principles electronic structure-based prediction of EI mass spectra in principle for any molecule. The systems in this case study are organic substances of nominal masses between 404 and 853 atomic mass units and cover a wide range of functional groups and organic molecular structure motifs. The results demonstrate the widespread applicability of the QCEIMS method for the unbiased computation of EI mass spectra even for larger molecules. Its strengths compared to standard (static) or database driven approaches in such cases are highlighted. Weak points regarding the required computation times or the approximate character of the employed QC methods are also discussed. We propose QCEIMS as a viable and robust way of predicting EI mass spectra for sizeable organic molecules relevant to medicinal and pharmaceutical chemistry.

  7. The laser desorption/laser ionization mass spectra of some anti-inflammatory drugs

    NASA Astrophysics Data System (ADS)

    Milnes, John; Rogers, Kevin; Jones, Sian; Gormally, John

    1994-03-01

    The IR laser desorption/ultraviolet laser ionization time-of-flight mass spectra are reported for the anti-inflammatory drugs indomethacin, acemetacin, ibuprofen, flurbiprofen, diflunisal and mefenamic acid. It is found that the six compounds can be readily ionized by two photon absorption at a fixed wavelength of 266 nm. Mass spectra have been obtained under conditions of high ionizing irradiance and the observed fragmentation behaviour is discussed.

  8. Mass measurement using energy spectra in three-body decays

    NASA Astrophysics Data System (ADS)

    Agashe, Kaustubh; Franceschini, Roberto; Kim, Doojin; Wardlow, Kyle

    2016-05-01

    In previous works we have demonstrated how the energy distribution of massless decay products in two body decays can be used to measure the mass of decaying particles. In this work we show how such results can be generalized to the case of multi-body decays. The key ideas that allow us to deal with multi-body final states are an extension of our previous results to the case of massive decay products and the factorization of the multi-body phase space. The mass measurement strategy that we propose is distinct from alternative methods because it does not require an accurate reconstruction of the entire event, as it does not involve, for instance, the missing transverse momentum, but rather requires measuring only the visible decay products of the decay of interest. To demonstrate the general strategy, we study a supersymmetric model wherein pair-produced gluinos each decay to a stable neutralino and a bottom quark-antiquark pair via an off -shell bottom squark. The combinatorial background stemming from the indistinguishable visible final states on both decay sides can be treated by an "event mixing" technique, the performance of which is discussed in detail. Taking into account dominant backgrounds, we are able to show that the mass of the gluino and, in favorable cases, that of the neutralino can be determined by this mass measurement strategy.

  9. Correlation of Multiple Peptide Mass Spectra for Phosphoprotein Identification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    When collision induced dissociation is used to fragment phosphorylated peptides during tandem mass spectrometry (MS2), an ion exhibiting the neutral loss of phosphoric acid can be the major product. The neutral loss ion can then be fragmented during MS3 for additional resolution of the peptide sequ...

  10. Mass measurement using energy spectra in three-body decays

    DOE PAGES

    Agashe, Kaustubh; Franceschini, Roberto; Kim, Doojin; Wardlow, Kyle

    2016-05-24

    In previous works we have demonstrated how the energy distribution of massless decay products in two body decays can be used to measure the mass of decaying particles. In this study, we show how such results can be generalized to the case of multi-body decays. The key ideas that allow us to deal with multi-body final states are an extension of our previous results to the case of massive decay products and the factorization of the multi-body phase space. The mass measurement strategy that we propose is distinct from alternative methods because it does not require an accurate reconstruction ofmore » the entire event, as it does not involve, for instance, the missing transverse momentum, but rather requires measuring only the visible decay products of the decay of interest. To demonstrate the general strategy, we study a supersymmetric model wherein pair-produced gluinos each decay to a stable neutralino and a bottom quark-antiquark pair via an off -shell bottom squark. The combinatorial background stemming from the indistinguishable visible final states on both decay sides can be treated by an “event mixing” technique, the performance of which is discussed in detail. In conclusion, taking into account dominant backgrounds, we are able to show that the mass of the gluino and, in favorable cases, that of the neutralino can be determined by this mass measurement strategy.« less

  11. Laser desorption/Fourier transform mass spectra of glycoalkaloids and steroid glycosides.

    PubMed

    Coates, M L; Wilkins, C L

    1986-04-01

    Positive- and negative-ion mass spectra of five glycoconjugates were obtained using laser desorption/Fourier transform mass spectrometry. These were the glycoalkaloids alpha-solanine and alpha-tomatine and the steroid glycosides gitoxin, lanatoside A and digitonin. Doping with KCl yielded both potassium- and chloride-attachment ions. Few fragment ions were observed for these species, with the exception of digitonin, although the negative-ion spectra showed relatively more fragmentation than the positive-ion spectra. All major fragments appeared to arise from losses of sugar groups due to cleavages at the glycosidic linkages. This contrasted sharply with the behavior of the malto-oligosaccharides studied in this laboratory.

  12. Mass spectra of heavy ions near comet Halley

    NASA Technical Reports Server (NTRS)

    Korth, A.; Richter, A. K.; Loidl, A.; Anderson, K. A.; Carlson, C. W.

    1986-01-01

    The heavy-ion analyzer, RPA2-PICCA, aboard the Giotto spacecraft, detected the first cometary ions at a distance of about 1.05 million km from the nucleus of comet Halley. In the inner coma the major ions identified are associated with the H2O, CO and CO2 groups. Ions of larger atomic mass unit are also present, corresponding possibly to various hydrocarbons, heavy metals of the iron-group or to sulphur compounds.

  13. Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles.

    PubMed

    Marty, Michael T; Baldwin, Andrew J; Marklund, Erik G; Hochberg, Georg K A; Benesch, Justin L P; Robinson, Carol V

    2015-04-21

    Interpretation of mass spectra is challenging because they report a ratio of two physical quantities, mass and charge, which may each have multiple components that overlap in m/z. Previous approaches to disentangling the two have focused on peak assignment or fitting. However, the former struggle with complex spectra, and the latter are generally computationally intensive and may require substantial manual intervention. We propose a new data analysis approach that employs a Bayesian framework to separate the mass and charge dimensions. On the basis of this approach, we developed UniDec (Universal Deconvolution), software that provides a rapid, robust, and flexible deconvolution of mass spectra and ion mobility-mass spectra with minimal user intervention. Incorporation of the charge-state distribution in the Bayesian prior probabilities provides separation of the m/z spectrum into its physical mass and charge components. We have evaluated our approach using systems of increasing complexity, enabling us to deduce lipid binding to membrane proteins, to probe the dynamics of subunit exchange reactions, and to characterize polydispersity in both protein assemblies and lipoprotein Nanodiscs. The general utility of our approach will greatly facilitate analysis of ion mobility and mass spectra.

  14. Spectral probabilities of top-down tandem mass spectra

    SciTech Connect

    Liu, Xiaowen; Segar, Matthew W.; Li, Shuai Cheng; Kim, Sangtae

    2014-01-24

    In mass spectrometry (MS)-based proteomics, accurate estimation of statistical signicance of peptide and protein identications is desired for determining whether they are actually correct. Probabilistic models, such as the generating function method, have been successfully applied to compute statistical signicance of peptide-spectrum matches (PSMs) in bottom-up MS, but it is limited to PSMs of short peptides without post-translational modications (PTMs). Recently, top-down MS has be- come available in many laboratories, which often identies intact proteins with PTMs. In this paper, we propose an extended generating function (EGF) method for accurately computing statistical signicance of protein- spectrum matches (PrSMs) with PTMs.

  15. Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification.

    PubMed

    Junqueira, Magno; Spirin, Victor; Santana Balbuena, Tiago; Waridel, Patrice; Surendranath, Vineeth; Kryukov, Grigoriy; Adzhubei, Ivan; Thomas, Henrik; Sunyaev, Shamil; Shevchenko, Andrej

    2008-08-01

    Only a small fraction of spectra acquired in LC-MS/MS runs matches peptides from target proteins upon database searches. The remaining, operationally termed background, spectra originate from a variety of poorly controlled sources and affect the throughput and confidence of database searches. Here, we report an algorithm and its software implementation that rapidly removes background spectra, regardless of their precise origin. The method estimates the dissimilarity distance between screened MS/MS spectra and unannotated spectra from a partially redundant background library compiled from several control and blank runs. Filtering MS/MS queries enhanced the protein identification capacity when searches lacked spectrum to sequence matching specificity. In sequence-similarity searches it reduced by, on average, 30-fold the number of orphan hits, which were not explicitly related to background protein contaminants and required manual validation. Removing high quality background MS/MS spectra, while preserving in the data set the genuine spectra from target proteins, decreased the false positive rate of stringent database searches and improved the identification of low-abundance proteins. PMID:18558732

  16. Identification of Ultramodified Proteins Using Top-Down Mass Spectra

    SciTech Connect

    Liu, Xiaowen; Hengel, Shawna M.; Wu, Si; Tolic, Nikola; Pasa-Tolic, Ljiljana; Pevzner, Pavel A.

    2013-11-05

    Post-translational modifications (PTMs) play an important role in various biological processes through changing protein structure and function. Some ultramodified proteins (like histones) have multiple PTMs forming PTM patterns that define the functionality of a protein. While bottom-up mass spectrometry (MS) has been successful in identifying individual PTMs within short peptides, it is unable to identify PTM patterns spread along entire proteins in a coordinated fashion. In contrast, top-down MS analyzes intact proteins and reveals PTM patterns along the entire proteins. However, while recent advances in instrumentation have made top-down MS accessible to many laboratories, most computational tools for top-down MS focus on proteins with few PTMs and are unable to identify complex PTM patterns. We propose a new algorithm, MS-Align-E, that identifies both expected and unexpected PTMs in ultramodified proteins. We demonstrate that MS-Align-E identifies many protein forms of histone H4 and benchmark it against the currently accepted software tools.

  17. High Pressure Mass Spectrometry: The Generation of Mass Spectra at Operating Pressures Exceeding 1 Torr in a Microscale Cylindrical Ion Trap.

    PubMed

    Blakeman, Kenion H; Wolfe, Derek W; Cavanaugh, Craig A; Ramsey, J Michael

    2016-05-17

    We present the first demonstration of high pressure mass spectrometry (HPMS), which we define as mass spectrometry performed at pressures greater than 100 mTorr. Mass analysis is shown at operational pressures exceeding 1 Torr of helium buffer gas. A differentially pumped MS system was constructed for HPMS development consisting of two chambers. The first chamber (mass analysis chamber) was operated at pressures up to 1.2 Torr and contained the ionization source and a microscale cylindrical ion trap (CIT) mass analyzer. The CIT had critical dimensions of r0 = 500 μm and z0 = 650 μm. The second chamber was held at a lower pressure (≤10 mTorr) and contained an electron multiplier for detection. Mass spectra for xenon, 2-chloroethyl ethyl sulfide (CEES), and octane were acquired with helium buffer gas pressures ranging from 0.04 to 1.2 Torr in the mass analysis chamber. Full-width at half-maximum of mass spectral peaks was found to increase 143% for xenon, 40% for CEES, and 77% for octane over this pressure range, with maximum peak widths of 1.19, 1.26, and 0.82 Da, respectively. Data were fitted with an algebraic model that factors in ion-neutral collision peak broadening effects at high pressures. Experimental and theoretical peak broadening slopes showed good agreement at buffer gas pressures greater than 0.2 Torr. Experiments presented here demonstrate mass spectrometry at pressures orders of magnitude higher than conventionally practiced with any type of mass analyzer. The use of HPMS provides a way to eliminate turbo pumping requirements, leading to significant reduction in MS system size, weight, and power and facilitating a path toward compact/hand-held mass spectrometers with numerous potential applications.

  18. High Pressure Mass Spectrometry: The Generation of Mass Spectra at Operating Pressures Exceeding 1 Torr in a Microscale Cylindrical Ion Trap.

    PubMed

    Blakeman, Kenion H; Wolfe, Derek W; Cavanaugh, Craig A; Ramsey, J Michael

    2016-05-17

    We present the first demonstration of high pressure mass spectrometry (HPMS), which we define as mass spectrometry performed at pressures greater than 100 mTorr. Mass analysis is shown at operational pressures exceeding 1 Torr of helium buffer gas. A differentially pumped MS system was constructed for HPMS development consisting of two chambers. The first chamber (mass analysis chamber) was operated at pressures up to 1.2 Torr and contained the ionization source and a microscale cylindrical ion trap (CIT) mass analyzer. The CIT had critical dimensions of r0 = 500 μm and z0 = 650 μm. The second chamber was held at a lower pressure (≤10 mTorr) and contained an electron multiplier for detection. Mass spectra for xenon, 2-chloroethyl ethyl sulfide (CEES), and octane were acquired with helium buffer gas pressures ranging from 0.04 to 1.2 Torr in the mass analysis chamber. Full-width at half-maximum of mass spectral peaks was found to increase 143% for xenon, 40% for CEES, and 77% for octane over this pressure range, with maximum peak widths of 1.19, 1.26, and 0.82 Da, respectively. Data were fitted with an algebraic model that factors in ion-neutral collision peak broadening effects at high pressures. Experimental and theoretical peak broadening slopes showed good agreement at buffer gas pressures greater than 0.2 Torr. Experiments presented here demonstrate mass spectrometry at pressures orders of magnitude higher than conventionally practiced with any type of mass analyzer. The use of HPMS provides a way to eliminate turbo pumping requirements, leading to significant reduction in MS system size, weight, and power and facilitating a path toward compact/hand-held mass spectrometers with numerous potential applications. PMID:27109864

  19. Deconvolution of Soft Ionization Mass Spectra of Chlorinated Paraffins To Resolve Congener Groups.

    PubMed

    Yuan, Bo; Alsberg, Tomas; Bogdal, Christian; MacLeod, Matthew; Berger, Urs; Gao, Wei; Wang, Yawei; de Wit, Cynthia A

    2016-09-20

    We describe and illustrate a three-step data-processing approach that enables individual congener groups of chlorinated paraffins (CPs) to be resolved in mass spectra obtained from either of two soft ionization methods: electron capture negative ionization mass spectrometry (ECNI-MS) or atmospheric pressure chemical ionization mass spectrometry (APCI-MS). In the first step, general fragmentation pathways of CPs are deduced from analysis of mass spectra of individual CP congeners. In the second step, all possible fragment ions in the general fragmentation pathways of CPs with 10 to 20 carbon atoms are enumerated and compared to mass spectra of CP mixture standards, and a deconvolution algorithm is applied to identify fragment ions that are actually observed. In the third step, isotope permutations of the observed fragment ions are calculated and used to identify isobaric overlaps, so that mass intensities of individual CP congener groups can be deconvolved from the unresolved isobaric ion signal intensities in mass spectra. For a specific instrument, the three steps only need to be done once to enable deconvolution of CPs in unknown samples. This approach enables congener group-level resolution of CP mixtures in environmental samples, and it opens up the possibility for quantification of congener groups. PMID:27531279

  20. Selectivity of solid phase extraction of freshwater dissolved organic matter and its effect on ultrahigh resolution mass spectra.

    PubMed

    Raeke, Julia; Lechtenfeld, Oliver J; Wagner, Martin; Herzsprung, Peter; Reemtsma, Thorsten

    2016-07-13

    Solid phase extraction (SPE) is often used for enrichment and clean-up prior to analysis of dissolved organic matter (DOM) by electrospray ionization (ESI) coupled to ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). It is generally accepted that extraction by SPE is not quantitative with respect to carbon concentration. However, little information is available on the selectivity of different SPE sorbents and the resulting effect for the acquired DOM mass spectra. Freshwater samples were extracted by the widely used PPL, HLB and C18 sorbents and the molecular composition and size distribution of the DOM in the extracts and in the permeates was compared to the original sample. Dissolved organic carbon (DOC) recoveries ranged between 20% and 65% for the three tested SPE sorbents. Size-exclusion chromatography coupled to organic carbon detection (SEC-OCD) revealed that limited recovery by PPL and HLB was primarily due to incomplete elution of a fraction of apparent high molecular weight from the solid phase. In contrast, incomplete retention on the solid phase, mainly observed for the C18 cartridge, was attributed to a fraction of low molecular weight. The FT-ICR mass spectra of the original sample and the SPE extracts did not differ significantly in their molecular weight distribution, but they showed sorbent specific differences in the degree of oxygenation and saturation. We concluded that the selective enrichment of freshwater DOM by SPE is less critical for subsequent FT-ICR MS analysis, because those fractions that are not sufficiently recovered have comparatively small effects on the mass spectra. This was confirmed by the extraction of model compounds, showing that very polar and small molecules are poorly extracted, but also have a low response in ESI-MS. Of the three tested SPE cartridges the PPL material offered the best properties for DOM enrichment for subsequent FT-ICR MS analysis as it minimizes too strong and

  1. DeconMSn: A Software Tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

    SciTech Connect

    Mayampurath, Anoop M.; Jaitly, Navdeep; Purvine, Samuel O.; Monroe, Matthew E.; Auberry, Kenneth J.; Adkins, Joshua N.; Smith, Richard D.

    2008-04-01

    We present a new software tool for tandem MS analyses that: • accurately calculates the monoisotopic mass and charge of high–resolution parent ions • accurately operates regardless of the mass selected for fragmentation • performs independent of instrument settings • enables optimal selection of search mass tolerance for high mass accuracy experiments • is open source and thus can be tailored to individual needs • incorporates a SVM-based charge detection algorithm for analyzing low resolution tandem MS spectra • creates multiple output data formats (.dta, .MGF) • handles .RAW files and .mzXML formats • compatible with SEQUEST, MASCOT, X!Tandem

  2. Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes

    NASA Astrophysics Data System (ADS)

    Lu, Jonathan; Trnka, Michael J.; Roh, Soung-Hun; Robinson, Philip J. J.; Shiau, Carrie; Fujimori, Danica Galonic; Chiu, Wah; Burlingame, Alma L.; Guan, Shenheng

    2015-12-01

    Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise.

  3. The dynamical properties of E-ring particles derived from CDA impact mass spectra

    NASA Astrophysics Data System (ADS)

    Namikis, R.; Horanyi, M.; Postberg, F.; Srama, R.; Kempf, S.

    2014-12-01

    The Cosmic Dust Analyser (CDA) on the Cassini spacecraft has the unique capability to obtain mass spectra of individual ring particles hitting the detector. There is empirical evidence that the spectral signatures of Saturnian water ice particles are indicative of their impact speed. Based on a detailed analysis of mass spectra recorded by CDA at the same E ring location, but at different spacecraft speeds, we devised a technique to accurately determine the speeds of E ring particles hitting CDA. This will allow us for the first time to characterize the dynamical properties of the E ring particles, which is the prerequisite for an in-depth understanding of the ring dynamics.

  4. Improved mass resolution and mass accuracy in TOF-SIMS spectra and images using argon gas cluster ion beams.

    PubMed

    Shon, Hyun Kyong; Yoon, Sohee; Moon, Jeong Hee; Lee, Tae Geol

    2016-06-09

    The popularity of argon gas cluster ion beams (Ar-GCIB) as primary ion beams in time-of-flight secondary ion mass spectrometry (TOF-SIMS) has increased because the molecular ions of large organic- and biomolecules can be detected with less damage to the sample surfaces. However, Ar-GCIB is limited by poor mass resolution as well as poor mass accuracy. The inferior quality of the mass resolution in a TOF-SIMS spectrum obtained by using Ar-GCIB compared to the one obtained by a bismuth liquid metal cluster ion beam and others makes it difficult to identify unknown peaks because of the mass interference from the neighboring peaks. However, in this study, the authors demonstrate improved mass resolution in TOF-SIMS using Ar-GCIB through the delayed extraction of secondary ions, a method typically used in TOF mass spectrometry to increase mass resolution. As for poor mass accuracy, although mass calibration using internal peaks with low mass such as hydrogen and carbon is a common approach in TOF-SIMS, it is unsuited to the present study because of the disappearance of the low-mass peaks in the delayed extraction mode. To resolve this issue, external mass calibration, another regularly used method in TOF-MS, was adapted to enhance mass accuracy in the spectrum and image generated by TOF-SIMS using Ar-GCIB in the delayed extraction mode. By producing spectra analyses of a peptide mixture and bovine serum albumin protein digested with trypsin, along with image analyses of rat brain samples, the authors demonstrate for the first time the enhancement of mass resolution and mass accuracy for the purpose of analyzing large biomolecules in TOF-SIMS using Ar-GCIB through the use of delayed extraction and external mass calibration.

  5. Automatic Preocessing of Impact Ionization Mass Spectra Obtained by Cassini CDA

    NASA Astrophysics Data System (ADS)

    Villeneuve, M.

    2015-12-01

    Since Cassini's arrival at Saturn in 2004, the Comic Dust Analyzer (CDA) has recorded nearly 200,000 mass spectra of dust particles. A majority of this data has been collected in Saturn's diffuse E ring where sodium salts embedded in water ice particles indicate that many particles are in fact frozen droplets from Enceladus' subsurface ocean that have been expelled from cracks in the icy crust. So far only a small fraction of the obtained spectra have been processed because the steps in processing the spectra require human manipulation. We developed an automatic processing pipeline for CDA mass spectra which will consistently analyze this data. The preprocessing steps are to de-noise the spectra, determine and remove the baseline, calculate the correct stretch parameter, and finally to identify elements and compounds in the spectra. With the E ring constantly evolving due to embedded active moons, this data will provide valuable information about the source of the E ring, the subsurface of Saturn's ice moon Enceladus, as well as about the dynamics of the ring itself.

  6. Denoising peptide tandem mass spectra for spectral libraries: a Bayesian approach.

    PubMed

    Shao, Wenguang; Lam, Henry

    2013-07-01

    With the rapid accumulation of data from shotgun proteomics experiments, it has become feasible to build comprehensive and high-quality spectral libraries of tandem mass spectra of peptides. A spectral library condenses experimental data into a retrievable format and can be used to aid peptide identification by spectral library searching. A key step in spectral library building is spectrum denoising, which is best accomplished by merging multiple replicates of the same peptide ion into a consensus spectrum. However, this approach cannot be applied to "singleton spectra," for which only one observed spectrum is available for the peptide ion. We developed a method, based on a Bayesian classifier, for denoising peptide tandem mass spectra. The classifier accounts for relationships between peaks, and can be trained on the fly from consensus spectra and immediately applied to denoise singleton spectra, without hard-coded knowledge about peptide fragmentation. A linear regression model was also trained to predict the number of useful "signal" peaks in a spectrum, thereby obviating the need for arbitrary thresholds for peak filtering. This Bayesian approach accumulates weak evidence systematically to boost the discrimination power between signal and noise peaks, and produces readily interpretable conditional probabilities that offer valuable insights into peptide fragmentation behaviors. By cross validation, spectra denoised by this method were shown to retain more signal peaks, and have higher spectral similarities to replicates, than those filtered by intensity only.

  7. Instrumental improvements and sample preparations that enable reproducible, reliable acquisition of mass spectra from whole bacterial cells

    PubMed Central

    Alusta, Pierre; Buzatu, Dan; Williams, Anna; Cooper, Willie-Mae; Tarasenko, Olga; Dorey, R Cameron; Hall, Reggie; Parker, W Ryan; Wilkes, Jon G

    2015-01-01

    Rationale Rapid sub-species characterization of pathogens is required for timely responses in outbreak situations. Pyrolysis mass spectrometry (PyMS) has the potential to be used for this purpose. Methods However, in order to make PyMS practical for traceback applications, certain improvements related to spectrum reproducibility and data acquisition speed were required. The main objectives of this study were to facilitate fast detection (<30 min to analyze 6 samples, including preparation) and sub-species-level bacterial characterization based on pattern recognition of mass spectral fingerprints acquired from whole cells volatilized and ionized at atmospheric pressure. An AccuTOF DART mass spectrometer was re-engineered to permit ionization of low-volatility bacteria by means of Plasma Jet Ionization (PJI), in which an electric discharge, and, by extension, a plasma beam, impinges on sample cells. Results Instrumental improvements and spectral acquisition methodology are described. Performance of the re-engineered system was assessed using a small challenge set comprised of assorted bacterial isolates differing in identity by varying amounts. In general, the spectral patterns obtained allowed differentiation of all samples tested, including those of the same genus and species but different serotypes. Conclusions Fluctuations of ±15% in bacterial cell concentrations did not substantially compromise replicate spectra reproducibility. © 2015 National Center for Toxicological Research. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd. PMID:26443394

  8. Localization and mass spectra of various matter fields on scalar-tensor brane

    SciTech Connect

    Xie, Qun-Ying; Zhao, Zhen-Hua; Zhong, Yi; Yang, Jie; Zhou, Xiang-Nan

    2015-03-10

    Recently, a new scalar-tensor braneworld model was presented in [http://dx.doi.org/10.1103/PhysRevD.86.127502]. It not only solves the gauge hierarchy problem but also reproduces a correct Friedmann-like equation on the brane. In this new model, there are two different brane solutions, for which the mass spectra of gravity on the brane are the same. In this paper, we investigate localization and mass spectra of various bulk matter fields (i.e., scalar, vector, Kalb-Ramond, and fermion fields) on the brane. It is shown that the zero modes of all the matter fields can be localized on the positive tension brane under some conditions, and the mass spectra of each kind of bulk matter field for the two brane solutions are different except for some special cases, which implies that the two brane solutions are not physically equivalent. When the coupling constants between the dilaton and bulk matter fields take special values, the mass spectra for both solutions are the same, and the scalar and vector zero modes are localized on the negative tension brane, while the KR zero mode is still localized on the positive tension brane.

  9. HUMIDITY EFFECTS ON THE MASS SPECTRA OF SINGLE AEROSOL PARTICLES. (R823980)

    EPA Science Inventory

    On-line laser desorption ionization mass spectrometry has developed into a widely used method for chemical characterization of individual aerosol particles. In the present study, the spectra of laboratory-generated particles were obtained as a function of relative humidity to elu...

  10. CAPILLARY ELECTROPHORESIS-ELECTROSPRAY MASS SPECTRA OF THE HERBICIDES PARAQUAT AND DIQUAT

    EPA Science Inventory

    The positive ion electrospray mass spectra of the quaternary ammonium salt herbicides paraquat and diquat are examined by on-line separation with capillary electrophoresis (CE) and by direct infusion of the analytes. The analytes are separated by CE in 7-10 min at pH 3.9 in 50% m...

  11. MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra

    PubMed Central

    2014-01-01

    Today’s highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most widely used search engines were developed when high-resolution mass spectrometry data were not readily available for fragment ion masses, we have designed a scoring algorithm particularly suitable for high mass accuracy. Our algorithm, MS Amanda, is generally applicable to HCD, ETD, and CID fragmentation type data. The algorithm confidently explains more spectra at the same false discovery rate than Mascot or SEQUEST on examined high mass accuracy data sets, with excellent overlap and identical peptide sequence identification for most spectra also explained by Mascot or SEQUEST. MS Amanda, available at http://ms.imp.ac.at/?goto=msamanda, is provided free of charge both as standalone version for integration into custom workflows and as a plugin for the Proteome Discoverer platform. PMID:24909410

  12. Compound classification by computer treatment of low resolution mass spectra - Application to geochemical and environmental problems.

    NASA Technical Reports Server (NTRS)

    Smith, D. H.; Eglinton, G.

    1972-01-01

    A description is given of a development of computer analysis of low-resolution chromatographic-mass spectrometric data, which provides a preliminary classification of an unknown spectrum as a listing of candidate classes of compounds. This procedure, referred to as COMSOC (Classification of Mass Spectra on Computers), operates by converting an incoming unknown mass spectrum into a simplified key word which is then compared with each of the key words held in its reference file. The advantages of COMSOC in characterizing complex mixtures are emphasized.

  13. A Newly Developed Fluorescence Model for C2H6 v5 and Application to Cometary Spectra Acquired with NIRSPEC at Keck II

    NASA Technical Reports Server (NTRS)

    Radeva, Yana L.; Mumma, Michael J.; Villanueva, Geronimo L.; A?Hearn, Michael F.

    2011-01-01

    Accurate rotational temperatures are essential for extracting production rates for parent volatiles in comets. Two strong bands of ethane (v7 at 2985.39/cm and v5 at 2895.67/cm) are seen in infrared cometary spectra, but the Q-branches of v7 are not resolved by current instruments and cannot provide an accurate rotational temperature with current models.We developed a fluorescence model for the C2H6 v5 band that can be used to derive a rotational temperature.We applied our C2H6 5 model to high-resolution infrared spectra of the comets C/2004 Q2 Machholz and C/2000 WM1 (LINEAR), acquired with the Near-infrared Echelle Spectrograph on the Keck II telescope. We demonstrate agreement among the rotational temperatures derived from C2H6 v5 and other species, and between mixing ratios derived from C2H6 v5 and C2H6 v7. As a symmetric hydrocarbon, C2H6 is observed only in the infrared, and it is now the fifth molecule (along with H2O, HCN, CO, and H2CO) for which we can derive a reliable rotational temperature from cometary infrared spectra.

  14. Mass spectra of the particle-antiparticle system with a Dirac oscillator interaction

    NASA Technical Reports Server (NTRS)

    Moshinsky, M.; Loyola, G.

    1993-01-01

    The present view about the structure of mesons is that they are a quark-antiquark system. The mass spectrum corresponding to this system should, in principle, be given by chromodynamics, but this turns out to be a complex affair. Thus it is of some interest to consider relativistic systems of particle-antiparticle, with a simple type of interaction, which could give some insight on the spectra we can expect for mesons. This analysis is carried out when the interaction is of the Dirac oscillator type. It is shown that the Dirac equation of the antiparticle can be obtained from that of the particle by just changing the frequency omega into -omega. Following a procedure suggested by Barut, the equation for the particle-antiparticle system is derived and it is solved by a perturbation procedure. Thus, explicit expressions for the square of the mass spectra are obtained and its implications in the meson case is discussed.

  15. Measuring nickel masses in Type Ia supernovae using cobalt emission in nebular phase spectra

    NASA Astrophysics Data System (ADS)

    Childress, Michael J.; Hillier, D. John; Seitenzahl, Ivo; Sullivan, Mark; Maguire, Kate; Taubenberger, Stefan; Scalzo, Richard; Ruiter, Ashley; Blagorodnova, Nadejda; Camacho, Yssavo; Castillo, Jayden; Elias-Rosa, Nancy; Fraser, Morgan; Gal-Yam, Avishay; Graham, Melissa; Howell, D. Andrew; Inserra, Cosimo; Jha, Saurabh W.; Kumar, Sahana; Mazzali, Paolo A.; McCully, Curtis; Morales-Garoffolo, Antonia; Pandya, Viraj; Polshaw, Joe; Schmidt, Brian; Smartt, Stephen; Smith, Ken W.; Sollerman, Jesper; Spyromilio, Jason; Tucker, Brad; Valenti, Stefano; Walton, Nicholas; Wolf, Christian; Yaron, Ofer; Young, D. R.; Yuan, Fang; Zhang, Bonnie

    2015-12-01

    The light curves of Type Ia supernovae (SNe Ia) are powered by the radioactive decay of 56Ni to 56Co at early times, and the decay of 56Co to 56Fe from ˜60 d after explosion. We examine the evolution of the [Co III] λ5893 emission complex during the nebular phase for SNe Ia with multiple nebular spectra and show that the line flux follows the square of the mass of 56Co as a function of time. This result indicates both efficient local energy deposition from positrons produced in 56Co decay and long-term stability of the ionization state of the nebula. We compile SN Ia nebular spectra from the literature and present 21 new late-phase spectra of 7 SNe Ia, including SN 2014J. From these we measure the flux in the [Co III] λ5893 line and remove its well-behaved time dependence to infer the initial mass of 56Ni (MNi) produced in the explosion. We then examine 56Ni yields for different SN Ia ejected masses (Mej - calculated using the relation between light-curve width and ejected mass) and find that the 56Ni masses of SNe Ia fall into two regimes: for narrow light curves (low stretch s ˜ 0.7-0.9), MNi is clustered near MNi ≈ 0.4 M⊙ and shows a shallow increase as Mej increases from ˜1 to 1.4 M⊙; at high stretch, Mej clusters at the Chandrasekhar mass (1.4 M⊙) while MNi spans a broad range from 0.6 to 1.2 M⊙. This could constitute evidence for two distinct SN Ia explosion mechanisms.

  16. A Sounding Rocket Mission Concept to Acquire High-Resolution Radiometric Spectra Spanning the 9 nm - 31 nm Wavelength Range

    NASA Technical Reports Server (NTRS)

    Krause, L. Habash; Cirtain, Jonathan; McGuirck, Michael; Pavelitz, Steven; Weber, Ed.; Winebarger, Amy

    2012-01-01

    When studying Solar Extreme Ultraviolet (EUV) emissions, both single-wavelength, two- dimensional (2D) spectroheliograms and multi-wavelength, one-dimensional (1D) line spectra are important, especially for a thorough understanding of the complex processes in the solar magnetized plasma from the base of the chromosphere through the corona. 2D image data are required for a detailed study of spatial structures, whereas radiometric (i.e., spectral) data provide information on relevant atomic excitation/ionization state densities (and thus temperature). Using both imaging and radiometric techniques, several satellite missions presently study solar dynamics in the EUV, including the Solar Dynamics Observatory (SDO), Hinode, and the Solar-Terrestrial Relations Observatory (STEREO). The EUV wavelengths of interest typically span 9 nm to 31 nm, with the shorter wavelengths being associated with the hottest features (e.g., intense flares and bright points) and the longer wavelengths associated with cooler features (e.g., coronal holes and filaments). Because the optical components of satellite instruments degrade over time, it is not uncommon to conduct sounding rocket underflights for calibration purposes. The authors have designed a radiometric sounding rocket payload that could serve as both a calibration underflight for and a complementary scientific mission to the upcoming Solar Ultraviolet Imager (SUVI) mission aboard the GOES-R satellite (scheduled for a 2015 launch). The challenge to provide quality radiometric line spectra over the 9-31 nm range covered by SUVI was driven by the multilayer coatings required to make the optical components, including mirrors and gratings, reflective over the entire range. Typically, these multilayers provide useful EUV reflectances over bandwidths of a few nm. Our solution to this problem was to employ a three-telescope system in which the optical components were coated with multilayers that spanned three wavelength ranges to cover

  17. The laser desorption/laser ionization mass spectra of some methylated xanthines and the laser desorption of caffeine and theophylline from thin layer chromatography plates

    NASA Astrophysics Data System (ADS)

    Rogers, Kevin; Milnes, John; Gormally, John

    1993-02-01

    Laser desorption/laser ionization time-of-flight mass spectra of caffeine, theophylline, theobromine and xanthine are reported. These mass spectra are compared with published spectra obtained using electron impact ionization. Mass spectra of caffeine and theophylline obtained by IR laser desorption from thin layer chromatography plates are also described. The laser desorption of materials from thin layer chromatography plates is discussed.

  18. Evolution of organic aerosol mass spectra upon heating: implications for OA phase and partitioning behavior

    SciTech Connect

    UC Davis; Cappa, Christopher D.; Wilson, Kevin R.

    2010-10-28

    Vacuum Ultraviolet (VUV) photoionization mass spectrometry has been used to measure the evolution of chemical composition for two distinct organic aerosol types as they are passed through a thermodenuder at different temperatures. The two organic aerosol types considered are primary lubricating oil (LO) aerosol and secondary aerosol from the alpha-pinene + O3 reaction (alphaP). The evolution of the VUV mass spectra for the two aerosol types with temperature are observed to differ dramatically. For LO particles, the spectra exhibit distinct changes with temperature in which the lower m/z peaks, corresponding to compounds with higher vapor pressures, disappear more rapidly than the high m/z peaks. In contrast, the alphaP aerosol spectrum is essentially unchanged by temperature even though the particles experience significant mass loss due to evaporation. The variations in the LO spectra are found to be quantitatively in agreement with expectations from absorptive partitioning theory whereas the alphaP spectra suggest that the evaporation of alphaP derived aerosol appears to not be governed by partitioning theory. We postulate that this difference arises from the alphaP particles existing as in a glassy state instead of having the expected liquid-like behavior. To reconcile these observations with decades of aerosol growth measurements, which indicate that OA formation is described by equilibrium partitioning, we present a conceptual model wherein the secondary OA is formed and then rapidly converted from an absorbing form to a non-absorbing form. The results suggest that although OA growth may be describable by equilibrium partitioning theory, the properties of organic aerosol once formed may differ significantly from the properties determined in the equilibrium framework.

  19. Excited state mass spectra of doubly heavy baryons {Ω _{cc}}, {Ω _{bb}}, and {Ω _{bc}}

    NASA Astrophysics Data System (ADS)

    Shah, Zalak; Thakkar, Kaushal; Rai, Ajay Kumar

    2016-10-01

    We discuss the mass spectrum of Ω baryon with two heavy quarks and one light quark ( ccs, bbs, and bcs). The main goal of the paper is to calculate the ground state masses and after that, the positive and negative parity excited states masses are also obtained within a hypercentral constituent quark model, using Coulomb plus linear potential framework. We also added a first order correction to the potential. The mass spectra up to 5S for radial excited states and 1P-5P, 1D-4D, and 1F-2F states for orbital excited states are computed for Ω _{cc}, Ω _{bb}, and Ω _{bc} baryons. Our obtained results are compared with other theoretical predictions, which could be a useful complementary tool for the interpretation of experimentally unknown heavy baryon spectra. The Regge trajectory is constructed in both the (n_r, M2) and the ( J, M2) planes for Ω _{cc}, Ω _{bb}, and Ω _{bc} baryons and their slopes and intercepts are also determined. Magnetic moments of doubly heavy Ω 's are also calculated.

  20. Towards automated discrimination of lipids versus peptides from full scan mass spectra

    PubMed Central

    Dittwald, Piotr; Nghia, Vu Trung; Harris, Glenn A.; Caprioli, Richard M.; Van de Plas, Raf; Laukens, Kris; Gambin, Anna; Valkenborg, Dirk

    2014-01-01

    Although physicochemical fractionation techniques play a crucial role in the analysis of complex mixtures, they are not necessarily the best solution to separate specific molecular classes, such as lipids and peptides. Any physical fractionation step such as, for example, those based on liquid chromatography, will introduce its own variation and noise. In this paper we investigate to what extent the high sensitivity and resolution of contemporary mass spectrometers offers viable opportunities for computational separation of signals in full scan spectra. We introduce an automatic method that can discriminate peptide from lipid peaks in full scan mass spectra, based on their isotopic properties. We systematically evaluate which features maximally contribute to a peptide versus lipid classification. The selected features are subsequently used to build a random forest classifier that enables almost perfect separation between lipid and peptide signals without requiring ion fragmentation and classical tandem MS-based identification approaches. The classifier is trained on in silico data, but is also capable of discriminating signals in real world experiments. We evaluate the influence of typical data inaccuracies of common classes of mass spectrometry instruments on the optimal set of discriminant features. Finally, the method is successfully extended towards the classification of individual lipid classes from full scan mass spectral features, based on input data defined by the Lipid Maps Consortium. PMID:25414814

  1. Automated identification by computer of the mass spectra of drugs in urine or serum extracts.

    PubMed

    Smith, N B

    1994-01-01

    Gas chromatography/mass spectrometry (GC/MS) is the method of choice for confirming the presence of drugs tentatively identified in urine or serum by thin-layer chromatography, gas chromatography, or immunoassay. One of the most widely used GC/MS systems is the Hewlett-Packard (HP) Model 5970 mass selective detector equipped with a work station programmed in Pascal. Searching of mass spectra after a GC/MS run must be done manually, and this can take hours, especially when there are many peaks in a chromatogram to check. I have developed software that allows the unattended searching of all peaks in a run, using a forward search algorithm with a custom-made drug library developed over a period of 5 years, and a reverse search with a 1600+ drug library from HP or another in-house drug library. Using these libraries with the two algorithms maximizes the chances of finding a drug peak and identifying it correctly. Individual searches take about 5 seconds each. Overall search time of nearly 200 mass spectra per run takes about 40 minutes, including printing time. This software has proven to be both labor saving and effective in positively identifying drugs. PMID:8127079

  2. Automated reduction and interpretation of multidimensional mass spectra for analysis of complex peptide mixtures

    NASA Astrophysics Data System (ADS)

    Gambin, Anna; Dutkowski, Janusz; Karczmarski, Jakub; Kluge, Boguslaw; Kowalczyk, Krzysztof; Ostrowski, Jerzy; Poznanski, Jaroslaw; Tiuryn, Jerzy; Bakun, Magda; Dadlez, Michal

    2007-01-01

    Here we develop a fully automated procedure for the analysis of liquid chromatography-mass spectrometry (LC-MS) datasets collected during the analysis of complex peptide mixtures. We present the underlying algorithm and outcomes of several experiments justifying its applicability. The novelty of our approach is to exploit the multidimensional character of the datasets. It is common knowledge that highly complex peptide mixtures can be analyzed by liquid chromatography coupled with mass spectrometry, but we are not aware of any existing automated MS spectra interpretation procedure designed to take into account the multidimensional character of the data. Our work fills this gap by providing an effective algorithm for this task, allowing for automated conversion of raw data to the list of masses of peptides.

  3. A model for quasi-parity-doublet spectra in odd-mass nuclei

    NASA Astrophysics Data System (ADS)

    Minkov, Nikolay

    2013-05-01

    A model of a quadrupole-octupole vibrating and rotating core plus a particle is proposed to describe and classify the quasi-parity-doublet spectra in odd-mass nuclei. The yrast levels are described as low-energy rotation-vibration modes built on the ground state. The non-yrast split parity-doublet sequences are considered as higher-energy rotation-vibration modes coupled to one-quasi-particle states. The even-even core is considered within the model of a coherent quadrupole-octupole motion, while the odd nucleon is described within the reflection-asymmetric deformed shell model with pairing interaction. The Coriolis decoupling and K-mixing interactions are calculated microscopically through a parity projection of the single-particle wave function. The unified model scheme was tested on the yrast and non-yrast quasi-parity-doublet spectra in the nuclei 223Ra and 221Fr.

  4. Spectral investigations of 2,5-difluoroaniline by using mass, electronic absorption, NMR, and vibrational spectra

    NASA Astrophysics Data System (ADS)

    Kose, Etem; Karabacak, Mehmet; Bardak, Fehmi; Atac, Ahmet

    2016-11-01

    One of the most significant aromatic amines is aniline, a primary aromatic amine replacing one hydrogen atom of a benzene molecule with an amino group (NH2). This study reports experimental and theoretical investigation of 2,5-difluoroaniline molecule (2,5-DFA) by using mass, ultraviolet-visible (UV-vis), 1H and 13C nuclear magnetic resonance (NMR), Fourier transform infrared and Raman (FT-IR and FT-Raman) spectra, and supported with theoretical calculations. Mass spectrum (MS) of 2,5-DFA is presented with their stabilities. The UV-vis spectra of the molecule are recorded in the range of 190-400 nm in water and ethanol solvents. The 1H and 13C NMR chemical shifts are recorded in CDCl3 solution. The vibrational spectra are recorded in the region 4000-400 cm-1 (FT-IR) and 4000-10 cm-1 (FT-Raman), respectively. Theoretical studies are underpinned the experimental results as described below; 2,5-DFA molecule is optimized by using B3LYP/6-311++G(d,p) basis set. The mass spectrum is evaluated and possible fragmentations are proposed based on the stable structure. The electronic properties, such as excitation energies, oscillator strengths, wavelengths, frontier molecular orbitals (FMO), HOMO and LUMO energies, are determined by time-dependent density functional theory (TD-DFT). The electrostatic potential surface (ESPs), density of state (DOS) diagrams are also prepared and evaluated. In addition to these, reduced density gradient (RDG) analysis is performed, and thermodynamic features are carried out theoretically. The NMR spectra (1H and 13C) are calculated by using the gauge-invariant atomic orbital (GIAO) method. The vibrational spectra of 2,5-DFA molecule are obtained by using DFT/B3LYP method with 6-311++G(d,p) basis set. Fundamental vibrations are assigned based on the potential energy distribution (PED) of the vibrational modes. The nonlinear optical properties (NLO) are also investigated. The theoretical and experimental results give a detailed description of

  5. Broad screening and identification of β-agonists in feed and animal body fluid and tissues using ultra-high performance liquid chromatography-quadrupole-orbitrap high resolution mass spectrometry combined with spectra library search.

    PubMed

    Li, Tingting; Cao, Jingjing; Li, Zhen; Wang, Xian; He, Pingli

    2016-02-01

    Broad screening and identification of β-agonists in feed, serum, urine, muscle and liver samples was achieved in a quick and highly sensitive manner using ultra high performance liquid chromatography-quadrupole-orbitrap high resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS) combined with a spectra library search. Solid-phase extraction technology was employed for sample purification and enrichment. After extraction and purification, the samples were analyzed using a Q-Orbitrap high-resolution mass spectrometer under full-scan and data-dependent MS/MS mode. The acquired mass spectra were compared with an in-house library (compound library and MS/MS mass spectral library) built with TraceFinder Software which contained the M/Z of the precursor ion, chemical formula, retention time, character fragment ions and the entire MS/MS spectra of 32 β-agonist standards. Screening was achieved by comparing 5 key mass spectral results and positive matches were marked. Using the developed method, the identification results from 10 spiked samples and 238 actual samples indicated that only 2% of acquired mass spectra produced false identities. The method validation results showed that the limit of detection ranged from 0.021-3.854 μg kg(-1)and 0.015-1.198 ng mL(-1) for solid and liquid samples, respectively.

  6. Mass spectra deconvolution of low, medium, and high volatility biogenic secondary organic aerosol.

    PubMed

    Kostenidou, Evangelia; Lee, Byong-Hyoek; Engelhart, Gabriella J; Pierce, Jeffrey R; Pandis, Spyros N

    2009-07-01

    Secondary organic aerosol (SOA) consists of compounds with a wide range of volatilities and its ambient concentration is sensitive to this volatility distribution. Recent field studies have shown that the typical mass spectrum of ambient oxygenated organic aerosol (OOA) as measured by the Aerodyne Aerosol Mass Spectrometer (AMS) is quite different from the SOA mass spectra reported in smog chamber experiments. Part of this discrepancy is due to the dependence of SOA composition on the organic aerosol concentration. High precursor concentrations lead to higher concentrations of the more volatile species in the produced SOA while at lower concentrations the less volatile compounds dominate the SOA composition. alpha-Pinene, beta-pinene, d-limonene, and beta-caryophyllene ozonolysis experiments were performed at moderate concentration levels. Using a thermodenuder the more volatile SOA species were removed achieving even lower SOA concentration. The less volatile fraction was then chemically characterized by an AMS. The signal fraction of m/z44, and thus the concentration of C02+, is significantly higher for the less volatile SOA. High NO(x) conditions result in less oxidized SOA than low NO(x) conditions, while increasing relative humidity levels results in more oxidized products for limonene but has little effect on alpha-and beta-pinene SOA. Combining a smog chamber with a thermodenuder model employing the volatility basis-set framework, the AMS SOA mass spectrum for each experiment and for each precursor is deconvoluted into low, medium, and high volatility component mass spectra. The spectrum of the surrogate component with the lower volatility is quite similar to that of ambient OOA.

  7. AUTOMATED DETERMINATION OF PRECURSOR ION, PRODUCT ION, AND NEUTRAL LOSS COMPOSITIONS AND DECONVOLUTION OF COMPOSITE MASS SPECTRA USING ION CORRELATION BASED ON EXACT MASSES AND RELATIVE ISOTOPIC ABUNDANCES

    EPA Science Inventory

    After a dispersive event, rapid determination of elemental compositions of ions in mass spectra is essential for tentatively identifying compounds. A Direct Analysis in Real Time (DART)® ion source interfaced to a JEOL AccuTOF® mass spectrometer provided exact masses accurate to ...

  8. Broken S flavor symmetry of leptons and quarks: Mass spectra and flavor mixing patterns

    NASA Astrophysics Data System (ADS)

    Xing, Zhi-zhong; Yang, Deshan; Zhou, Shun

    2010-06-01

    We apply the discrete S3 flavor symmetry to both lepton and quark sectors of the Standard Model extended by introducing one Higgs triplet and realizing the type-II seesaw mechanism for finite neutrino masses. The resultant mass matrices of charged leptons (Ml), neutrinos (Mν), up-type quarks (Mu) and down-type quarks (Md) have a universal form consisting of two terms: one is proportional to the identity matrix I and the other is proportional to the democracy matrix D. We argue that the textures of Ml, Mu and Md are dominated by the D term, while that of Mν is dominated by the I term. This hypothesis implies a near mass degeneracy of three neutrinos and can naturally explain why the mass matrices of charged fermions are strongly hierarchical, why the quark mixing matrix is close to I and why the lepton mixing matrix contains two large angles. We discuss a rather simple perturbation ansatz to break the S3 symmetry and obtain more realistic mass spectra of leptons and quarks as well as their flavor mixing patterns. We stress that the I term, which used to be ignored from Ml, Mu and Md, is actually important because it can significantly modify the smallest lepton flavor mixing angle θ13 or three quark flavor mixing angles.

  9. Accurate and Efficient Resolution of Overlapping Isotopic Envelopes in Protein Tandem Mass Spectra

    PubMed Central

    Xiao, Kaijie; Yu, Fan; Fang, Houqin; Xue, Bingbing; Liu, Yan; Tian, Zhixin

    2015-01-01

    It has long been an analytical challenge to accurately and efficiently resolve extremely dense overlapping isotopic envelopes (OIEs) in protein tandem mass spectra to confidently identify proteins. Here, we report a computationally efficient method, called OIE_CARE, to resolve OIEs by calculating the relative deviation between the ideal and observed experimental abundance. In the OIE_CARE method, the ideal experimental abundance of a particular overlapping isotopic peak (OIP) is first calculated for all the OIEs sharing this OIP. The relative deviation (RD) of the overall observed experimental abundance of this OIP relative to the summed ideal value is then calculated. The final individual abundance of the OIP for each OIE is the individual ideal experimental abundance multiplied by 1 + RD. Initial studies were performed using higher-energy collisional dissociation tandem mass spectra on myoglobin (with direct infusion) and the intact E. coli proteome (with liquid chromatographic separation). Comprehensive data at the protein and proteome levels, high confidence and good reproducibility were achieved. The resolving method reported here can, in principle, be extended to resolve any envelope-type overlapping data for which the corresponding theoretical reference values are available. PMID:26439836

  10. PepArML: A Meta-Search Peptide Identification Platform for Tandem Mass Spectra.

    PubMed

    Edwards, Nathan J

    2013-12-01

    The PepArML meta-search peptide identification platform for tandem mass spectra provides a unified search interface to seven search engines; a robust cluster, grid, and cloud computing scheduler for large-scale searches; and an unsupervised, model-free, machine-learning-based result combiner, which selects the best peptide identification for each spectrum, estimates false-discovery rates, and outputs pepXML format identifications. The meta-search platform supports Mascot; Tandem with native, k-score and s-score scoring; OMSSA; MyriMatch; and InsPecT with MS-GF spectral probability scores—reformatting spectral data and constructing search configurations for each search engine on the fly. The combiner selects the best peptide identification for each spectrum based on search engine results and features that model enzymatic digestion, retention time, precursor isotope clusters, mass accuracy, and proteotypic peptide properties, requiring no prior knowledge of feature utility or weighting. The PepArML meta-search peptide identification platform often identifies two to three times more spectra than individual search engines at 10% FDR.

  11. Hadron Mass Spectra and Decay Rates in a Potential Model with Relativistic Wave Equations.

    NASA Astrophysics Data System (ADS)

    Namgung, Wuk

    Hadron properties of mass spectra and decay rates are calculated in a quark potential model. Wave equations based on the Klein-Gordon and Todorov equations both of which incorporate the feature of relativistic two-body kinematics are used. The wave equations are modified to contain potentials which transform either like a Lorentz scalar or like a time-component of a four-vector. Potentials based on the Fogleman-Lichtenberg-Wills potential which has the properties suggested by QCD of both confinement and asymptotic freedom are used. The potentials, motivated by QCD but otherwise phenomenological, are further generalized to forms which can apply to any color representation. To break the degeneracy between vector and pseudoscalar mesons or between spin-3/2 and spin-1/2 baryons, the essential feature of spin dependence is included in the potentials. The masses of vector and pseudoscalar mesons are calculated with only a small number of adjustable parameters, and good qualitative agreement with experiment is obtained for both heavy and light mesons. Baryons are treated in this framework by making use of a quark-diquark two-body model of baryons. First, diquark properties are calculated without any additional parameters. The g-factors of diquarks and spin-flavor configuration of baryons, which are necessary for the calculation of baryons, are given. Then baryon masses are calculated also without additional parameters. The results of the masses of ground-state baryons are in good qualitative agreement with experiment. Also effective constituent quark masses are obtained using current quark masses as input. The calculated effective constituent quark masses are in the right range of the values that most theoretical estimates have given. The general qualitative features of hadron spectra are similar with the two relativistic wave equations, although there are differences in detail. The Van Royen-Weisskopf formula for electromagnetic decay widths of vector mesons into lepton

  12. Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra.

    PubMed

    Wang, Jian; Anania, Veronica G; Knott, Jeff; Rush, John; Lill, Jennie R; Bourne, Philip E; Bandeira, Nuno

    2014-04-01

    The combination of chemical cross-linking and mass spectrometry has recently been shown to constitute a powerful tool for studying protein-protein interactions and elucidating the structure of large protein complexes. However, computational methods for interpreting the complex MS/MS spectra from linked peptides are still in their infancy, making the high-throughput application of this approach largely impractical. Because of the lack of large annotated datasets, most current approaches do not capture the specific fragmentation patterns of linked peptides and therefore are not optimal for the identification of cross-linked peptides. Here we propose a generic approach to address this problem and demonstrate it using disulfide-bridged peptide libraries to (i) efficiently generate large mass spectral reference data for linked peptides at a low cost and (ii) automatically train an algorithm that can efficiently and accurately identify linked peptides from MS/MS spectra. We show that using this approach we were able to identify thousands of MS/MS spectra from disulfide-bridged peptides through comparison with proteome-scale sequence databases and significantly improve the sensitivity of cross-linked peptide identification. This allowed us to identify 60% more direct pairwise interactions between the protein subunits in the 20S proteasome complex than existing tools on cross-linking studies of the proteasome complexes. The basic framework of this approach and the MS/MS reference dataset generated should be valuable resources for the future development of new tools for the identification of linked peptides. PMID:24493012

  13. Acquiring Structural Information on Virus Particles with Charge Detection Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Keifer, David Z.; Motwani, Tina; Teschke, Carolyn M.; Jarrold, Martin F.

    2016-06-01

    Charge detection mass spectrometry (CDMS) is a single-molecule technique particularly well-suited to measuring the mass and charge distributions of heterogeneous, MDa-sized ions. In this work, CDMS has been used to analyze the assembly products of two coat protein variants of bacteriophage P22. The assembly products show broad mass distributions extending from 5 to 15 MDa for A285Y and 5 to 25 MDa for A285T coat protein variants. Because the charge of large ions generated by electrospray ionization depends on their size, the charge can be used to distinguish hollow shells from more compact structures. A285T was found to form T = 4 and T = 7 procapsids, and A285Y makes a small number of T = 3 and T = 4 procapsids. Owing to the decreased stability of the A285Y and A285T particles, chemical cross-linking was required to stabilize them for electrospray CDMS. Graphical Abstract[Figure not available: see fulltext.

  14. Factor analysis of combined organic and inorganic aerosol mass spectra from high resolution aerosol mass spectrometer measurements

    NASA Astrophysics Data System (ADS)

    Sun, Y. L.; Zhang, Q.; Schwab, J. J.; Yang, T.; Ng, N. L.; Demerjian, K. L.

    2012-09-01

    Positive matrix factorization (PMF) was applied to the merged high resolution mass spectra of organic and inorganic aerosols from aerosol mass spectrometer (AMS) measurements to investigate the sources and evolution processes of submicron aerosols in New York City in summer 2009. This new approach is able to study the distribution of organic and inorganic species in different types of aerosols, the acidity of organic aerosol (OA) factors, and the fragment ion patterns related to photochemical processing. In this study, PMF analysis of the unified AMS spectral matrix resolved 8 factors. The hydrocarbon-like OA (HOA) and cooking OA (COA) factors contain negligible amounts of inorganic species. The two factors that are primarily ammonium sulfate (SO4-OA) and ammonium nitrate (NO3-OA), respectively, are overall neutralized. Among all OA factors the organic fraction of SO4-OA shows the highest degree of oxidation (O/C = 0.69). Two semi-volatile oxygenated OA (OOA) factors, i.e., a less oxidized (LO-OOA) and a more oxidized (MO-OOA), were also identified. MO-OOA represents local photochemical products with a diurnal profile exhibiting a pronounced noon peak, consistent with those of formaldehyde (HCHO) and Ox(= O3 + NO2). The NO+/NO2+ ion ratio in MO-OOA is much higher than that in NO3-OA and in pure ammonium nitrate, indicating the formation of organic nitrates. The nitrogen-enriched OA (NOA) factor contains ~25% of acidic inorganic salts, suggesting the formation of secondary OA via acid-base reactions of amines. The size distributions of OA factors derived from the size-resolved mass spectra show distinct diurnal evolving behaviors but overall a progressing evolution from smaller to larger particle mode as the oxidation degree of OA increases. Our results demonstrate that PMF analysis of the unified aerosol mass spectral matrix which contains both inorganic and organic aerosol signals may enable the deconvolution of more OA factors and gain more insights into the

  15. Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

    PubMed

    Wenger, Craig D; Boyne, Michael T; Ferguson, Jonathan T; Robinson, Dana E; Kelleher, Neil L

    2008-11-01

    For automated production of tandem mass spectrometric data for proteins and peptides >3 kDa at >50 000 resolution, a dual online-offline approach is presented here that improves upon standard liquid chromatography-tandem mass spectrometry (LC-MS/MS) strategies. An integrated hardware and software infrastructure analyzes online LC-MS data and intelligently determines which targets to interrogate offline using a posteriori knowledge such as prior observation, identification, and degree of characterization. This platform represents a way to implement accurate mass inclusion and exclusion lists in the context of a proteome project, automating collection of high-resolution MS/MS data that cannot currently be acquired on a chromatographic time scale at equivalent spectral quality. For intact proteins from an acid extract of human nuclei fractionated by reversed-phase liquid chromatography (RPLC), the automated offline system generated 57 successful identifications of protein forms arising from 30 distinct genes, a substantial improvement over online LC-MS/MS using the same 12 T LTQ FT Ultra instrument. Analysis of human nuclei subjected to a shotgun Lys-C digest using the same RPLC/automated offline sampling identified 147 unique peptides containing 29 co- and post-translational modifications. Expectation values ranged from 10 (-5) to 10 (-99), allowing routine multiplexed identifications. PMID:18841935

  16. Energy spectra of massive two-body decay products and mass measurement

    NASA Astrophysics Data System (ADS)

    Agashe, Kaustubh; Franceschini, Roberto; Hong, Sungwoo; Kim, Doojin

    2016-04-01

    We have recently established a new method for measuring the mass of unstable particles produced at hadron colliders based on the analysis of the energy distribution of a mass less product from their two-body decays. The central ingredient of our proposal is the remarkable result that, for an unpolarized decaying particle, the location of the peak in the energy distribution of the observed decay product is identical to the (fixed) value of the energy that this particle would have in the rest-frame of the decaying particle, which, in turn, is a simple function of the involved masses. In addition, we utilized the property that this energy distribution is symmetric around the location of peak when energy is plotted on a logarithmic scale. The general strategy was demonstrated in several specific cases, including both beyond the standard model particles, as well as for the top quark. In the present work, we generalize this method to the case of a massive decay product from a two-body decay; this procedure is far from trivial because (in general) both the above-mentioned properties are no longer valid. Nonetheless, we propose a suitably modified parametrization of the energy distribution that was used successfully for the massless case, which can deal with the massive case as well. We test this parametrization on concrete examples of energy spectra of Z bosons from the decay of a heavier supersymmetric partner of top quark (stop) into a Z boson and a lighter stop. After establishing the accuracy of this parametrization, we study a realistic application for the same process, but now including dominant backgrounds and using foreseeable statistics at LHC14, in order to determine the performance of this method for an actual mass measurement. The upshot of our present and previous work is that, in spite of energy being a Lorentz-variant quantity, its distribution emerges as a powerful tool for mass measurement at hadron colliders.

  17. Generalized focus point and mass spectra comparison of highly natural SUGRA GUT models

    NASA Astrophysics Data System (ADS)

    Baer, Howard; Barger, Vernon; Savoy, Michael

    2016-04-01

    Supergravity grand unified models (SUGRA GUTs) are highly motivated and allow for a high degree of electroweak naturalness when the superpotential parameter μ ˜100 - 300 GeV (preferring values closer to 100 GeV). We first illustrate that models with radiatively driven naturalness enjoy a generalized focus-point behavior wherein all soft terms are correlated instead of just scalar masses. Next, we generate spectra from four SUGRA GUT archetypes: 1. S O (10 ) models where the Higgs doublets live in different ten-dimensional irreducible representations (irreps), 2. models based on S O (10 ) where the Higgs multiplets live in a single ten-dimensional irrep but with D -term scalar mass splitting, 3. models based on S U (5 ), and 4. a more general SUGRA model with 12 independent parameters. Electroweak naturalness implies for all models a spectrum of light Higgsinos with mW˜1,Z˜ 1 ,2≲300 GeV and gluinos with mg ˜≲ 2 - 4 TeV . However, masses and mixing in the third generation sfermion sector differ distinctly between the models. These latter differences would be most easily tested at a linear e+e- collider with √{s }˜ multi-TeV scale but measurements at a 50-100 TeV hadron collider are also possible.

  18. Absorption, fluorescence, and Raman spectra of mass-selected rhenium dimers in argon matrices

    NASA Astrophysics Data System (ADS)

    Hu, Zhendong; Dong, Jian-Guo; Lombardi, John R.; Lindsay, D. M.; Harbich, W.

    1994-07-01

    We report absorption, laser fluorescence, and Raman spectra for Re2 in an argon matrix prepared by the mass-selected ion deposition technique. The dirhenium absorption spectrum consists of seven band systems (A-G) extending from the near infrared into the ultraviolet region. For the A system (a simple vibrational progression), we find T0=10 817(1) cm-1, ωe=317.1(5) cm-1 and ωexe=1.0(1) cm-1. A Franck-Condon analysis of the A system intensities predicts that this state has a smaller equilibrium internuclear distance than the ground state (Δre=-0.073 Å), in violation of Badger's rule. The B system starts at 13 250 cm-1 and consists of four overlapping (and possibly perturbed) subsystems, whose average vibrational spacing is 270(11) cm-1. The C, D, E, and F systems (vibrational spacings in parentheses) are centered at 22 300 cm-1 (210 cm-1), 24 500 cm-1 (195 cm-1), 29 150 cm-1 (175 cm-1), and 32 900 cm-1 (160 cm-1), respectively. Weak fluorescence spectra, obtained upon laser excitation into the A system, were characterized by vibrational progressions to the dimer ground (X) state and to a low lying (X') state for which T0=357.6(5) cm-1 and ωe=332.3(2) cm-1. Raman and fluorescence progressions to the ground state were observed when the B system was excited. These data give ωe=337.9(49) cm-1 for the dimer ground state in good agreement with measurements from photodetachment spectra [J. Am. Chem. Soc. 108, 178 (1986)]. We propose likely assignments for the low lying electronic states of Re2 and discuss our results in terms of the bonding in the other group VIIB dimers, Mn2 and Tc2.

  19. Preliminary results of investigations into the use of artificial neural networks for discriminating gas chromatograph mass spectra of remote samples

    NASA Technical Reports Server (NTRS)

    Geller, Harold A.; Norris, Eugene; Warnock, Archibald, III

    1991-01-01

    Neural networks trained using mass spectra data from the National Institute of Standards and Technology (NIST) are studied. The investigations also included sample data from the gas chromatograph mass spectrometer (GCMS) instrument aboard the Viking Lander, obtained from the National Space Science Data Center. The work performed to data and the preliminary results from the training and testing of neural networks are described. These preliminary results are presented for the purpose of determining the viability of applying artificial neural networks in discriminating mass spectra samples from remote instrumentation such as the Mars Rover Sample Return Mission and the Cassini Probe.

  20. Energy spectra of massive two-body decay products and mass measurement

    DOE PAGES

    Agashe, Kaustubh; Franceschini, Roberto; Hong, Sungwoo; Kim, Doojin

    2016-04-26

    Here, we have recently established a new method for measuring the mass of unstable particles produced at hadron colliders based on the analysis of the energy distribution of a massless product from their two-body decays. The central ingredient of our proposal is the remarkable result that, for an unpolarized decaying particle, the location of the peak in the energy distribution of the observed decay product is identical to the (fixed) value of the energy that this particle would have in the rest-frame of the decaying particle, which, in turn, is a simple function of the involved masses. In addition, wemore » utilized the property that this energy distribution is symmetric around the location of peak when energy is plotted on a logarithmic scale. The general strategy was demonstrated in several specific cases, including both beyond the standard model particles, as well as for the top quark. In the present work, we generalize this method to the case of a massive decay product from a two-body decay; this procedure is far from trivial because (in general) both the above-mentioned properties are no longer valid. Nonetheless, we propose a suitably modified parametrization of the energy distribution that was used successfully for the massless case, which can deal with the massive case as well. We test this parametrization on concrete examples of energy spectra of Z bosons from the decay of a heavier supersymmetric partner of top quark (stop) into a Z boson and a lighter stop. After establishing the accuracy of this parametrization, we study a realistic application for the same process, but now including dominant backgrounds and using foreseeable statistics at LHC14, in order to determine the performance of this method for an actual mass measurement. The upshot of our present and previous work is that, in spite of energy being a Lorentz-variant quantity, its distribution emerges as a powerful tool for mass measurement at hadron colliders.« less

  1. Synchronized Polarization Induced Electrospray: Comprehensively Profiling Biomolecules in Single Cells by Combining both Positive-Ion and Negative-Ion Mass Spectra.

    PubMed

    Hu, Jun; Jiang, Xiao-Xiao; Wang, Jiang; Guan, Qi-Yuan; Zhang, Pan-Ke; Xu, Jing-Juan; Chen, Hong-Yuan

    2016-07-19

    In this work, a synchronized polarization induced electrospray ionization (SPI-ESI) method is developed and applied for the analysis of single-cell samples. In SPI-ESI, periodic alternating current square wave voltage (AC-SWV) is applied to induce the bipolar spray and both positive-ion and negative-ion mass spectra are obtained through one measurement by synchronizing the mode of mass analyzer with the bipolar spray process. Compared with conventional nanoelectrospray ionization (nESI, flow rate < 1000 nL/min), ultralow spray flow rate (pico-electrospray ionization, pESI, flow rate < 1000 pL/min) is achieved in SPI-ESI without loss of its sensitivity. The decrease of flow rate prolongs the MS signal duration from single-cell samples to acquire ms(2) data for components determination. To our knowledge, this is the first time to successfully achieve comprehensive analysis of single-cell samples by combining both positive-ion and negative-ion mass spectra. Ultimately, 86 components are profiled from single Allium cepa cells and 94 components are profiled from single PC-12 cells. PMID:27297455

  2. Light and Heavy Cosmic-Ray Mass Group Energy Spectra as Measured by the MAKET-ANI Detector

    NASA Astrophysics Data System (ADS)

    Chilingarian, A.; Gharagyozyan, G.; Hovsepyan, G.; Ghazaryan, S.; Melkumyan, L.; Vardanyan, A.

    2004-03-01

    Standard models of cosmic-ray origin link the space accelerators of our Galaxy to the supernova remnants (SNRs)-expanding shells driven by very fast blast waves, usually with gamma-ray pulsars near the morphological center. Energy spectra of fully stripped ions with charges from Z=1 to Z=26 can provide clues to the validity of the standard model. Unfortunately, smeared data from the extensive air shower experiments do not provide enough information for such ion ``spectroscopy.'' Nonetheless, the measurement of energy spectra of two or three broad mass groups (so-called light, intermediate, and heavy) will allow us to prove or disprove the ``rigidity-dependent'' acceleration. Recently, using multidimensional classification methods, the ``all-particle'' spectra from the MAKET-ANI experiment on Mount Aragats, in Armenia, was categorized into two distinct primary mass groups. We present, for the first time, the light and heavy nuclei spectra from the MAKET-ANI experiment.

  3. Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output.

    PubMed

    Turewicz, Michael; Deutsch, Eric W

    2011-01-01

    This chapter describes Mass Spectrometry Markup Language (mzML), an XML-based and vendor-neutral standard data format for storage and exchange of mass spectrometer output like raw spectra and peak lists. It is intended to replace its two precursor data formats (mzData and mzXML), which had been developed independently a few years earlier. Hence, with the release of mzML, the problem of having two different formats for the same purposes is solved, and with it the duplicated effort of maintaining and supporting two data formats. The new format has been developed by a broad-based consortium of major instrument vendors, software vendors, and academic researchers under the aegis of the Human Proteome Organisation (HUPO), Proteomics Standards Initiative (PSI), with full participation of the main developers of the precursor formats. This comprehensive approach helped mzML to become a generally accepted standard. Furthermore, the collaborative development insured that mzML has adopted the best features of its precursor formats. In this chapter, we discuss mzML's development history, its design principles and use cases, as well as its main building components. We also present the available documentation, an example file, and validation software for mzML. PMID:21063948

  4. Dielectron Mass Spectra from Au +Au Collisions at √sNN =200 GeV

    NASA Astrophysics Data System (ADS)

    Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; Aggarwal, M. M.; Ahammed, Z.; Alekseev, I.; Alford, J.; Anson, C. D.; Aparin, A.; Arkhipkin, D.; Aschenauer, E. C.; Averichev, G. S.; Banerjee, A.; Barnovska, Z.; Beavis, D. R.; Bellwied, R.; Bhasin, A.; Bhati, A. K.; Bhattarai, P.; Bichsel, H.; Bielcik, J.; Bielcikova, J.; Bland, L. C.; Bordyuzhin, I. G.; Borowski, W.; Bouchet, J.; Brandin, A. V.; Brovko, S. G.; Bültmann, S.; Bunzarov, I.; Burton, T. P.; Butterworth, J.; Caines, H.; Calderón de la Barca Sánchez, M.; Cebra, D.; Cendejas, R.; Cervantes, M. C.; Chaloupka, P.; Chang, Z.; Chattopadhyay, S.; Chen, H. F.; Chen, J. H.; Chen, L.; Cheng, J.; Cherney, M.; Chikanian, A.; Christie, W.; Chwastowski, J.; Codrington, M. J. M.; Cramer, J. G.; Crawford, H. J.; Cui, X.; Das, S.; Davila Leyva, A.; De Silva, L. C.; Debbe, R. R.; Dedovich, T. G.; Deng, J.; Derevschikov, A. A.; Derradi de Souza, R.; Dhamija, S.; di Ruzza, B.; Didenko, L.; Dilks, C.; Ding, F.; Djawotho, P.; Dong, X.; Drachenberg, J. L.; Draper, J. E.; Du, C. M.; Dunkelberger, L. E.; Dunlop, J. C.; Efimov, L. G.; Engelage, J.; Engle, K. S.; Eppley, G.; Eun, L.; Evdokimov, O.; Fatemi, R.; Fazio, S.; Fedorisin, J.; Filip, P.; Finch, E.; Fisyak, Y.; Flores, C. E.; Gagliardi, C. A.; Gangadharan, D. R.; Garand, D.; Geurts, F.; Gibson, A.; Girard, M.; Gliske, S.; Grosnick, D.; Guo, Y.; Gupta, A.; Gupta, S.; Guryn, W.; Haag, B.; Hajkova, O.; Hamed, A.; Han, L.-X.; Haque, R.; Harris, J. W.; Heppelmann, S.; Hirsch, A.; Hoffmann, G. W.; Hofman, D. J.; Horvat, S.; Huang, B.; Huang, H. Z.; Huang, X.; Huck, P.; Humanic, T. J.; Igo, G.; Jacobs, W. W.; Jang, H.; Judd, E. G.; Kabana, S.; Kalinkin, D.; Kang, K.; Kauder, K.; Ke, H. W.; Keane, D.; Kechechyan, A.; Kesich, A.; Khan, Z. H.; Kikola, D. P.; Kisel, I.; Kisiel, A.; Koetke, D. D.; Kollegger, T.; Konzer, J.; Koralt, I.; Korsch, W.; Kotchenda, L.; Kravtsov, P.; Krueger, K.; Kulakov, I.; Kumar, L.; Kycia, R. A.; Lamont, M. A. C.; Landgraf, J. M.; Landry, K. D.; Lauret, J.; Lebedev, A.; Lednicky, R.; Lee, J. H.; LeVine, M. J.; Li, C.; Li, W.; Li, X.; Li, X.; Li, Y.; Li, Z. M.; Lima, L. M.; Lisa, M. A.; Liu, F.; Ljubicic, T.; Llope, W. J.; Longacre, R. S.; Luo, X.; Ma, G. L.; Ma, Y. G.; Madagodagettige Don, D. M. M. D.; Mahapatra, D. P.; Majka, R.; Margetis, S.; Markert, C.; Masui, H.; Matis, H. S.; McDonald, D.; McShane, T. S.; Minaev, N. G.; Mioduszewski, S.; Mohanty, B.; Mondal, M. M.; Morozov, D. A.; Munhoz, M. G.; Mustafa, M. K.; Nandi, B. K.; Nasim, Md.; Nayak, T. K.; Nelson, J. M.; Nogach, L. V.; Noh, S. Y.; Novak, J.; Nurushev, S. B.; Odyniec, G.; Ogawa, A.; Oh, K.; Ohlson, A.; Okorokov, V.; Oldag, E. W.; Oliveira, R. A. N.; Pachr, M.; Page, B. S.; Pal, S. K.; Pan, Y. X.; Pandit, Y.; Panebratsev, Y.; Pawlak, T.; Pawlik, B.; Pei, H.; Perkins, C.; Peryt, W.; Pile, P.; Planinic, M.; Pluta, J.; Plyku, D.; Poljak, N.; Porter, J.; Poskanzer, A. M.; Pruthi, N. K.; Przybycien, M.; Pujahari, P. R.; Qiu, H.; Quintero, A.; Ramachandran, S.; Raniwala, R.; Raniwala, S.; Ray, R. L.; Riley, C. K.; Ritter, H. G.; Roberts, J. B.; Rogachevskiy, O. V.; Romero, J. L.; Ross, J. F.; Roy, A.; Ruan, L.; Rusnak, J.; Sahoo, N. R.; Sahu, P. K.; Sakrejda, I.; Salur, S.; Sandacz, A.; Sandweiss, J.; Sangaline, E.; Sarkar, A.; Schambach, J.; Scharenberg, R. P.; Schmah, A. M.; Schmidke, W. B.; Schmitz, N.; Seger, J.; Seyboth, P.; Shah, N.; Shahaliev, E.; Shanmuganathan, P. V.; Shao, M.; Sharma, B.; Shen, W. Q.; Shi, S. S.; Shou, Q. Y.; Sichtermann, E. P.; Singaraju, R. N.; Skoby, M. J.; Smirnov, D.; Smirnov, N.; Solanki, D.; Sorensen, P.; deSouza, U. G.; Spinka, H. M.; Srivastava, B.; Stanislaus, T. D. S.; Stevens, J. R.; Stock, R.; Strikhanov, M.; Stringfellow, B.; Suaide, A. A. P.; Sumbera, M.; Sun, X.; Sun, X. M.; Sun, Y.; Sun, Z.; Surrow, B.; Svirida, D. N.; Symons, T. J. M.; Szanto de Toledo, A.; Takahashi, J.; Tang, A. H.; Tang, Z.; Tarnowsky, T.; Thomas, J. H.; Timmins, A. R.; Tlusty, D.; Tokarev, M.; Trentalange, S.; Tribble, R. E.; Tribedy, P.; Trzeciak, B. A.; Tsai, O. D.; Turnau, J.; Ullrich, T.; Underwood, D. G.; Van Buren, G.; van Nieuwenhuizen, G.; Vanfossen, J. A.; Varma, R.; Vasconcelos, G. M. S.; Vasiliev, A. N.; Vertesi, R.; Videbæk, F.; Viyogi, Y. P.; Vokal, S.; Vossen, A.; Wada, M.; Wang, F.; Wang, G.; Wang, H.; Wang, J. S.; Wang, X. L.; Wang, Y.; Wang, Y.; Webb, G.; Webb, J. C.; Westfall, G. D.; Wieman, H.; Wissink, S. W.; Witt, R.; Wu, Y. F.; Xiao, Z.; Xie, W.; Xin, K.; Xu, H.; Xu, N.; Xu, Q. H.; Xu, Y.; Xu, Z.; Yan, W.; Yang, C.; Yang, Y.; Yang, Y.; Ye, Z.; Yepes, P.; Yi, L.; Yip, K.; Yoo, I.-K.; Zawisza, Y.; Zbroszczyk, H.; Zha, W.; Zhang, J. B.; Zhang, J. L.; Zhang, S.; Zhang, X. P.; Zhang, Y.; Zhang, Z. P.; Zhao, F.; Zhao, J.; Zhong, C.; Zhu, X.; Zhu, Y. H.; Zoulkarneeva, Y.; Zyzak, M.; STAR Collaboration

    2014-07-01

    We report the STAR measurements of dielectron (e+e-) production at midrapidity (|yee|<1) in Au +Au collisions at √sNN =200 GeV. The measurements are evaluated in different invariant mass regions with a focus on 0.30-0.76 (ρ-like), 0.76-0.80 (ω-like), and 0.98-1.05 (ϕ-like) GeV /c2. The spectrum in the ω-like and ϕ-like regions can be well described by the hadronic cocktail simulation. In the ρ-like region, however, the vacuum ρ spectral function cannot describe the shape of the dielectron excess. In this range, an enhancement of 1.77±0.11(stat)±0.24(syst)±0.33(cocktail) is determined with respect to the hadronic cocktail simulation that excludes the ρ meson. The excess yield in the ρ-like region increases with the number of collision participants faster than the ω and ϕ yields. Theoretical models with broadened ρ contributions through interactions with constituents in the hot QCD medium provide a consistent description of the dilepton mass spectra for the measurement presented here and the earlier data at the Super Proton Synchrotron energies.

  5. DtaRefinery, a Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Data Sets*

    PubMed Central

    Petyuk, Vladislav A.; Mayampurath, Anoop M.; Monroe, Matthew E.; Polpitiya, Ashoka D.; Purvine, Samuel O.; Anderson, Gordon A.; Camp, David G.; Smith, Richard D.

    2010-01-01

    Hybrid two-stage mass spectrometers capable of both highly accurate mass measurement and high throughput MS/MS fragmentation have become widely available in recent years, allowing for significantly better discrimination between true and false MS/MS peptide identifications by the application of a relatively narrow window for maximum allowable deviations of measured parent ion masses. To fully gain the advantage of highly accurate parent ion mass measurements, it is important to limit systematic mass measurement errors. Based on our previous studies of systematic biases in mass measurement errors, here, we have designed an algorithm and software tool that eliminates the systematic errors from the peptide ion masses in MS/MS data. We demonstrate that the elimination of the systematic mass measurement errors allows for the use of tighter criteria on the deviation of measured mass from theoretical monoisotopic peptide mass, resulting in a reduction of both false discovery and false negative rates of peptide identification. A software implementation of this algorithm called DtaRefinery reads a set of fragmentation spectra, searches for MS/MS peptide identifications using a FASTA file containing expected protein sequences, fits a regression model that can estimate systematic errors, and then corrects the parent ion mass entries by removing the estimated systematic error components. The output is a new file with fragmentation spectra with updated parent ion masses. The software is freely available. PMID:20019053

  6. FUV Spectra of Evolved Late-K and M Stars: Mass Loss Revisited and Stellar Activity

    NASA Technical Reports Server (NTRS)

    Harper, Graham M.

    2002-01-01

    This is the final report for the FUSE Cycle 1 program A100: FUV Spectra of Evolved Late-K and M Stars: Mass Loss revisited and Stellar Activity. Targets alpha TrA (K3 II) and gamma Cru (M3 III) were originally assigned 25 ksec each, to be observed in the medium aperture. Once the in-flight performance and telescope alignment problems were known, the observations were reprogrammed to optimized the scientific return of the program. Alpha TrA was scheduled for 25 ksec observations in both the medium and large apertures. The principle aim of this program was to measure the stellar FUV line and continuum emission, in order to estimate the photoionization radiation field and to determine the level of stellar activity through the fluxes in the collisionally excited high temperature diagnostics: C III 977Angstroms and O VI 1032,1038Angstrom doublet. The medium aperture observations were obtained successfully while the large aperture observations were thought by Johns Hopkins University (JHU)to be lost to satellite problems. There was insufficient signal-to- noise in the medium aperture short wavelength Sic channels to do quantitative science.

  7. Measurement of branching fractions and mass spectra of B-->Kpipigamma.

    PubMed

    Aubert, B; Barate, R; Boutigny, D; Couderc, F; Karyotakis, Y; Lees, J P; Poireau, V; Tisserand, V; Zghiche, A; Grauges, E; Palano, A; Pappagallo, M; Pompili, A; Chen, J C; Qi, N D; Rong, G; Wang, P; Zhu, Y S; Eigen, G; Ofte, I; Stugu, B; Abrams, G S; Battaglia, M; Breon, A B; Brown, D N; Button-Shafer, J; Cahn, R N; Charles, E; Day, C T; Gill, M S; Gritsan, A V; Groysman, Y; Jacobsen, R G; Kadel, R W; Kadyk, J; Kerth, L T; Kolomensky, Yu G; Kukartsev, G; Lynch, G; Mir, L M; Oddone, P J; Orimoto, T J; Pripstein, M; Roe, N A; Ronan, M T; Wenzel, W A; Barrett, M; Ford, K E; Harrison, T J; Hart, A J; Hawkes, C M; Morgan, S E; Watson, A T; Fritsch, M; Goetzen, K; Held, T; Koch, H; Lewandowski, B; Pelizaeus, M; Peters, K; Schroeder, T; Steinke, M; Boyd, J T; Burke, J P; Chevalier, N; Cottingham, W N; Kelly, M P; Cuhadar-Donszelmann, T; Fulsom, B G; Hearty, C; Knecht, N S; Mattison, T S; McKenna, J A; Khan, A; Kyberd, P; Saleem, M; Teodorescu, L; Blinov, A E; Blinov, V E; Bukin, A D; Druzhinin, V P; Golubev, V B; Kravchenko, E A; Onuchin, A P; Serednyakov, S I; Skovpen, Yu I; Solodov, E P; Yushkov, A N; Best, D; Bondioli, M; Bruinsma, M; Chao, M; Eschrich, I; Kirkby, D; Lankford, A J; Mandelkern, M; Mommsen, R K; Roethel, W; Stoker, D P; Buchanan, C; Hartfiel, B L; Foulkes, S D; Gary, J W; Long, O; Shen, B C; Wang, K; Zhang, L; del Re, D; Hadavand, H K; Hill, E J; MacFarlane, D B; Paar, H P; Rahatlou, S; Sharma, V; Berryhill, J W; Campagnari, C; Cunha, A; Dahmes, B; Hong, T M; Mazur, M A; Richman, J D; Verkerke, W; Beck, T W; Eisner, A M; Flacco, C J; Heusch, C A; Kroseberg, J; Lockman, W S; Nesom, G; Schalk, T; Schumm, B A; Seiden, A; Spradlin, P; Williams, D C; Wilson, M G; Albert, J; Chen, E; Dubois-Felsmann, G P; Dvoretskii, A; Hitlin, D G; Narsky, I; Piatenko, T; Porter, F C; Ryd, A; Samuel, A; Andreassen, R; Jayatilleke, S; Mancinelli, G; Meadows, B T; Sokoloff, M D; Blanc, F; Bloom, P; Chen, S; Ford, W T; Nauenberg, U; Olivas, A; Rankin, P; Ruddick, W O; Smith, J G; Ulmer, K A; Wagner, S R; Zhang, J; Chen, A; Eckhart, E A; Soffer, A; Toki, W H; Wilson, R J; Zeng, Q; Altenburg, D; Feltresi, E; Hauke, A; Spaan, B; Brandt, T; Brose, J; Dickopp, M; Klose, V; Lacker, H M; Nogowski, R; Otto, S; Petzold, A; Schott, G; Schubert, J; Schubert, K R; Schwierz, R; Sundermann, J E; Bernard, D; Bonneaud, G R; Grenier, P; Schrenk, S; Thiebaux, Ch; Vasileiadis, G; Verderi, M; Bard, D J; Clark, P J; Gradl, W; Muheim, F; Playfer, S; Xie, Y; Andreotti, M; Azzolini, V; Bettoni, D; Bozzi, C; Calabrese, R; Cibinetto, G; Luppi, E; Negrini, M; Piemontese, L; Anulli, F; Baldini-Ferroli, R; Calcaterra, A; de Sangro, R; Finocchiaro, G; Patteri, P; Peruzzi, I M; Piccolo, M; Zallo, A; Buzzo, A; Capra, R; Contri, R; Lo Vetere, M; Macri, M; Monge, M R; Passaggio, S; Patrignani, C; Robutti, E; Santroni, A; Tosi, S; Bailey, S; Brandenburg, G; Chaisanguanthum, K S; Morii, M; Won, E; Wu, J; Dubitzky, R S; Langenegger, U; Marks, J; Schenk, S; Uwer, U; Bhimji, W; Bowerman, D A; Dauncey, P D; Egede, U; Flack, R L; Gaillard, J R; Morton, G W; Nash, J A; Nikolich, M B; Taylor, G P; Vazquez, W P; Charles, M J; Mader, W F; Mallik, U; Mohapatra, A K; Cochran, J; Crawley, H B; Eyges, V; Meyer, W T; Prell, S; Rosenberg, E I; Rubin, A E; Yi, J; Arnaud, N; Davier, M; Giroux, X; Grosdidier, G; Höcker, A; Le Diberder, F; Lepeltier, V; Lutz, A M; Oyanguren, A; Petersen, T C; Pierini, M; Plaszczynski, S; Rodier, S; Roudeau, P; Schune, M H; Stocchi, A; Wormser, G; Cheng, C H; Lange, D J; Simani, M C; Wright, D M; Bevan, A J; Chavez, C A; Coleman, J P; Forster, I J; Fry, J R; Gabathuler, E; Gamet, R; George, K A; Hutchcroft, D E; Parry, R J; Payne, D J; Schofield, K C; Touramanis, C; Cormack, C M; Di Lodovico, F; Sacco, R; Brown, C L; Cowan, G; Flaecher, H U; Green, M G; Hopkins, D A; Jackson, P S; McMahon, T R; Ricciardi, S; Salvatore, F; Brown, D; Davis, C L; Allison, J; Barlow, N R; Barlow, R J; Hodgkinson, M C; Lafferty, G D; Naisbit, M T; Williams, J C; Chen, C; Farbin, A; Hulsbergen, W D; Jawahery, A; Kovalskyi, D; Lae, C K; Lillard, V; Roberts, D A; Simi, G; Blaylock, G; Dallapiccola, C; Hertzbach, S S; Kofler, R; Koptchev, V B; Li, X; Moore, T B; Saremi, S; Staengle, H; Willocq, S; Cowan, R; Koeneke, K; Sciolla, G; Sekula, S J; Spitznagel, M; Taylor, F; Yamamoto, R K; Kim, H; Patel, P M; Robertson, S H; Lazzaro, A; Lombardo, V; Palombo, F; Bauer, J M; Cremaldi, L; Eschenburg, V; Godang, R; Kroeger, R; Reidy, J; Sanders, D A; Summers, D J; Zhao, H W; Brunet, S; Côté, D; Taras, P; Viaud, B; Nicholson, H; Cavallo, N; De Nardo, G; Fabozzi, F; Gatto, C; Lista, L; Monorchio, D; Paolucci, P; Piccolo, D; Sciacca, C; Baak, M; Bulten, H; Raven, G; Snoek, H L; Wilden, L; Jessop, C P; LoSecco, J M; Allmendinger, T; Benelli, G; Gan, K K; Honscheid, K; Hufnagel, D; Jackson, P D; Kagan, H; Kass, R; Pulliam, T; Rahimi, A M; Ter-Antonyan, R; Wong, Q K; Brau, J; Frey, R; Igonkina, O; Lu, M; Potter, C T; Sinev, N B; Strom, D; Strube, J; Torrence, E; Dorigo, A; Galeazzi, F; Margoni, M; Morandin, M; Posocco, M; Rotondo, M; Simonetto, F; Stroili, R; Voci, C; Benayoun, M; Briand, H; Chauveau, J; David, P; Del Buono, L; de la Vaissière, Ch; Hamon, O; John, M J J; Leruste, Ph; Malclès, J; Ocariz, J; Roos, L; Therin, G; Behera, P K; Gladney, L; Guo, Q H; Panetta, J; Biasini, M; Covarelli, R; Pacetti, S; Pioppi, M; Angelini, C; Batignani, G; Bettarini, S; Bucci, F; Calderini, G; Carpinelli, M; Cenci, R; Forti, F; Giorgi, M A; Lusiani, A; Marchiori, G; Morganti, M; Neri, N; Paoloni, E; Rama, M; Rizzo, G; Walsh, J; Haire, M; Judd, D; Wagoner, D E; Biesiada, J; Danielson, N; Elmer, P; Lau, Y P; Lu, C; Olsen, J; Smith, A J S; Telnov, A V; Bellini, F; Cavoto, G; D'Orazio, A; Di Marco, E; Faccini, R; Ferrarotto, F; Ferroni, F; Gaspero, M; Li Gioi, L; Mazzoni, M A; Morganti, S; Piredda, G; Polci, F; Safai Tehrani, F; Voena, C; Schröder, H; Wagner, G; Waldi, R; Adye, T; De Groot, N; Franek, B; Gopal, G P; Olaiya, E O; Wilson, F F; Aleksan, R; Emery, S; Gaidot, A; Ganzhur, S F; Giraud, P-F; Graziani, G; Hamel de Monchenault, G; Kozanecki, W; Legendre, M; London, G W; Mayer, B; Vasseur, G; Yèche, Ch; Zito, M; Purohit, M V; Weidemann, A W; Wilson, J R; Yumiceva, F X; Abe, T; Allen, M T; Aston, D; Bartoldus, R; Berger, N; Boyarski, A M; Buchmueller, O L; Claus, R; Convery, M R; Cristinziani, M; Dingfelder, J C; Dong, D; Dorfan, J; Dujmic, D; Dunwoodie, W; Fan, S; Field, R C; Glanzman, T; Gowdy, S J; Hadig, T; Halyo, V; Hast, C; Hryn'ova, T; Innes, W R; Kelsey, M H; Kim, P; Kocian, M L; Leith, D W G S; Libby, J; Luitz, S; Luth, V; Lynch, H L; Marsiske, H; Messner, R; Muller, D R; O'Grady, C P; Ozcan, V E; Perazzo, A; Perl, M; Ratcliff, B N; Roodman, A; Salnikov, A A; Schindler, R H; Schwiening, J; Snyder, A; Stelzer, J; Su, D; Sullivan, M K; Suzuki, K; Swain, S; Thompson, J M; Va'vra, J; Weaver, M; Weinstein, A J R; Wisniewski, W J; Wittgen, M; Wright, D H; Yarritu, A K; Yi, K; Young, C C; Burchat, P R; Edwards, A J; Majewski, S A; Petersen, B A; Roat, C; Ahmed, M; Ahmed, S; Alam, M S; Ernst, J A; Saeed, M A; Wappler, F R; Zain, S B; Bugg, W; Krishnamurthy, M; Spanier, S M; Eckmann, R; Ritchie, J L; Satpathy, A; Schwitters, R F; Izen, J M; Kitayama, I; Lou, X C; Ye, S; Bianchi, F; Bona, M; Gallo, F; Gamba, D; Bomben, M; Bosisio, L; Cartaro, C; Cossutti, F; Della Ricca, G; Dittongo, S; Grancagnolo, S; Lanceri, L; Vitale, L; Martinez-Vidal, F; Panvini, R S; Banerjee, Sw; Bhuyan, B; Brown, C M; Fortin, D; Hamano, K; Kowalewski, R; Roney, J M; Sobie, R J; Back, J J; Harrison, P F; Latham, T E; Mohanty, G B; Band, H R; Chen, X; Cheng, B; Dasu, S; Datta, M; Eichenbaum, A M; Flood, K T; Graham, M; Hollar, J J; Johnson, J R; Kutter, P E; Li, H; Liu, R; Mellado, B; Mihalyi, A; Pan, Y; Prepost, R; Tan, P; von Wimmersperg-Toeller, J H; Wu, S L; Yu, Z; Neal, H

    2007-05-25

    We present a measurement of the partial branching fractions and mass spectra of the exclusive radiative penguin processes B-->Kpipigamma in the range m(Kpipi)<1.8 GeV/c(2). We reconstruct four final states: K(+)pi(-)pi(+)gamma, K(+)pi(-)pi(0)gamma, K(S)(0)pi(-)pi(+)gamma, and K(S)(0)pi(+)pi(0)gamma, where K(S)(0)-->pi(+)pi(-). Using 232 x 10(6) e(+)e(-)-->BB events recorded by the BABAR experiment at the SLAC PEP-II asymmetric-energy storage ring, we measure the branching fractions B(B(+)-->K(+)pi(-)pi(+)gamma)=[2.95+/-0.13(stat)+/-0.20(syst)] x 10(-5), B(B(0)-->K(+)pi(-)pi(0)gamma)=[4.07+/-0.22(stat)+/-0.31(syst)] x 10(-5), B(B(0)-->K(0)pi(+)pi(-)gamma)=[1.85+/-0.21(stat)+/-0.12(syst)] x 10(-5), and B(B(+)-->K(0)pi(+)pi(0)gamma)=[4.56+/-0.42(stat)+/-0.31(syst)] x 10(-5). PMID:17677766

  8. Faster and more accurate graphical model identification of tandem mass spectra using trellises

    PubMed Central

    Wang, Shengjie; Halloran, John T.; Bilmes, Jeff A.; Noble, William S.

    2016-01-01

    Tandem mass spectrometry (MS/MS) is the dominant high throughput technology for identifying and quantifying proteins in complex biological samples. Analysis of the tens of thousands of fragmentation spectra produced by an MS/MS experiment begins by assigning to each observed spectrum the peptide that is hypothesized to be responsible for generating the spectrum. This assignment is typically done by searching each spectrum against a database of peptides. To our knowledge, all existing MS/MS search engines compute scores individually between a given observed spectrum and each possible candidate peptide from the database. In this work, we use a trellis, a data structure capable of jointly representing a large set of candidate peptides, to avoid redundantly recomputing common sub-computations among different candidates. We show how trellises may be used to significantly speed up existing scoring algorithms, and we theoretically quantify the expected speedup afforded by trellises. Furthermore, we demonstrate that compact trellis representations of whole sets of peptides enables efficient discriminative learning of a dynamic Bayesian network for spectrum identification, leading to greatly improved spectrum identification accuracy. Contact: bilmes@uw.edu or william-noble@uw.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307634

  9. Measurement of branching fractions and mass spectra of B-->Kpipigamma.

    PubMed

    Aubert, B; Barate, R; Boutigny, D; Couderc, F; Karyotakis, Y; Lees, J P; Poireau, V; Tisserand, V; Zghiche, A; Grauges, E; Palano, A; Pappagallo, M; Pompili, A; Chen, J C; Qi, N D; Rong, G; Wang, P; Zhu, Y S; Eigen, G; Ofte, I; Stugu, B; Abrams, G S; Battaglia, M; Breon, A B; Brown, D N; Button-Shafer, J; Cahn, R N; Charles, E; Day, C T; Gill, M S; Gritsan, A V; Groysman, Y; Jacobsen, R G; Kadel, R W; Kadyk, J; Kerth, L T; Kolomensky, Yu G; Kukartsev, G; Lynch, G; Mir, L M; Oddone, P J; Orimoto, T J; Pripstein, M; Roe, N A; Ronan, M T; Wenzel, W A; Barrett, M; Ford, K E; Harrison, T J; Hart, A J; Hawkes, C M; Morgan, S E; Watson, A T; Fritsch, M; Goetzen, K; Held, T; Koch, H; Lewandowski, B; Pelizaeus, M; Peters, K; Schroeder, T; Steinke, M; Boyd, J T; Burke, J P; Chevalier, N; Cottingham, W N; Kelly, M P; Cuhadar-Donszelmann, T; Fulsom, B G; Hearty, C; Knecht, N S; Mattison, T S; McKenna, J A; Khan, A; Kyberd, P; Saleem, M; Teodorescu, L; Blinov, A E; Blinov, V E; Bukin, A D; Druzhinin, V P; Golubev, V B; Kravchenko, E A; Onuchin, A P; Serednyakov, S I; Skovpen, Yu I; Solodov, E P; Yushkov, A N; Best, D; Bondioli, M; Bruinsma, M; Chao, M; Eschrich, I; Kirkby, D; Lankford, A J; Mandelkern, M; Mommsen, R K; Roethel, W; Stoker, D P; Buchanan, C; Hartfiel, B L; Foulkes, S D; Gary, J W; Long, O; Shen, B C; Wang, K; Zhang, L; del Re, D; Hadavand, H K; Hill, E J; MacFarlane, D B; Paar, H P; Rahatlou, S; Sharma, V; Berryhill, J W; Campagnari, C; Cunha, A; Dahmes, B; Hong, T M; Mazur, M A; Richman, J D; Verkerke, W; Beck, T W; Eisner, A M; Flacco, C J; Heusch, C A; Kroseberg, J; Lockman, W S; Nesom, G; Schalk, T; Schumm, B A; Seiden, A; Spradlin, P; Williams, D C; Wilson, M G; Albert, J; Chen, E; Dubois-Felsmann, G P; Dvoretskii, A; Hitlin, D G; Narsky, I; Piatenko, T; Porter, F C; Ryd, A; Samuel, A; Andreassen, R; Jayatilleke, S; Mancinelli, G; Meadows, B T; Sokoloff, M D; Blanc, F; Bloom, P; Chen, S; Ford, W T; Nauenberg, U; Olivas, A; Rankin, P; Ruddick, W O; Smith, J G; Ulmer, K A; Wagner, S R; Zhang, J; Chen, A; Eckhart, E A; Soffer, A; Toki, W H; Wilson, R J; Zeng, Q; Altenburg, D; Feltresi, E; Hauke, A; Spaan, B; Brandt, T; Brose, J; Dickopp, M; Klose, V; Lacker, H M; Nogowski, R; Otto, S; Petzold, A; Schott, G; Schubert, J; Schubert, K R; Schwierz, R; Sundermann, J E; Bernard, D; Bonneaud, G R; Grenier, P; Schrenk, S; Thiebaux, Ch; Vasileiadis, G; Verderi, M; Bard, D J; Clark, P J; Gradl, W; Muheim, F; Playfer, S; Xie, Y; Andreotti, M; Azzolini, V; Bettoni, D; Bozzi, C; Calabrese, R; Cibinetto, G; Luppi, E; Negrini, M; Piemontese, L; Anulli, F; Baldini-Ferroli, R; Calcaterra, A; de Sangro, R; Finocchiaro, G; Patteri, P; Peruzzi, I M; Piccolo, M; Zallo, A; Buzzo, A; Capra, R; Contri, R; Lo Vetere, M; Macri, M; Monge, M R; Passaggio, S; Patrignani, C; Robutti, E; Santroni, A; Tosi, S; Bailey, S; Brandenburg, G; Chaisanguanthum, K S; Morii, M; Won, E; Wu, J; Dubitzky, R S; Langenegger, U; Marks, J; Schenk, S; Uwer, U; Bhimji, W; Bowerman, D A; Dauncey, P D; Egede, U; Flack, R L; Gaillard, J R; Morton, G W; Nash, J A; Nikolich, M B; Taylor, G P; Vazquez, W P; Charles, M J; Mader, W F; Mallik, U; Mohapatra, A K; Cochran, J; Crawley, H B; Eyges, V; Meyer, W T; Prell, S; Rosenberg, E I; Rubin, A E; Yi, J; Arnaud, N; Davier, M; Giroux, X; Grosdidier, G; Höcker, A; Le Diberder, F; Lepeltier, V; Lutz, A M; Oyanguren, A; Petersen, T C; Pierini, M; Plaszczynski, S; Rodier, S; Roudeau, P; Schune, M H; Stocchi, A; Wormser, G; Cheng, C H; Lange, D J; Simani, M C; Wright, D M; Bevan, A J; Chavez, C A; Coleman, J P; Forster, I J; Fry, J R; Gabathuler, E; Gamet, R; George, K A; Hutchcroft, D E; Parry, R J; Payne, D J; Schofield, K C; Touramanis, C; Cormack, C M; Di Lodovico, F; Sacco, R; Brown, C L; Cowan, G; Flaecher, H U; Green, M G; Hopkins, D A; Jackson, P S; McMahon, T R; Ricciardi, S; Salvatore, F; Brown, D; Davis, C L; Allison, J; Barlow, N R; Barlow, R J; Hodgkinson, M C; Lafferty, G D; Naisbit, M T; Williams, J C; Chen, C; Farbin, A; Hulsbergen, W D; Jawahery, A; Kovalskyi, D; Lae, C K; Lillard, V; Roberts, D A; Simi, G; Blaylock, G; Dallapiccola, C; Hertzbach, S S; Kofler, R; Koptchev, V B; Li, X; Moore, T B; Saremi, S; Staengle, H; Willocq, S; Cowan, R; Koeneke, K; Sciolla, G; Sekula, S J; Spitznagel, M; Taylor, F; Yamamoto, R K; Kim, H; Patel, P M; Robertson, S H; Lazzaro, A; Lombardo, V; Palombo, F; Bauer, J M; Cremaldi, L; Eschenburg, V; Godang, R; Kroeger, R; Reidy, J; Sanders, D A; Summers, D J; Zhao, H W; Brunet, S; Côté, D; Taras, P; Viaud, B; Nicholson, H; Cavallo, N; De Nardo, G; Fabozzi, F; Gatto, C; Lista, L; Monorchio, D; Paolucci, P; Piccolo, D; Sciacca, C; Baak, M; Bulten, H; Raven, G; Snoek, H L; Wilden, L; Jessop, C P; LoSecco, J M; Allmendinger, T; Benelli, G; Gan, K K; Honscheid, K; Hufnagel, D; Jackson, P D; Kagan, H; Kass, R; Pulliam, T; Rahimi, A M; Ter-Antonyan, R; Wong, Q K; Brau, J; Frey, R; Igonkina, O; Lu, M; Potter, C T; Sinev, N B; Strom, D; Strube, J; Torrence, E; Dorigo, A; Galeazzi, F; Margoni, M; Morandin, M; Posocco, M; Rotondo, M; Simonetto, F; Stroili, R; Voci, C; Benayoun, M; Briand, H; Chauveau, J; David, P; Del Buono, L; de la Vaissière, Ch; Hamon, O; John, M J J; Leruste, Ph; Malclès, J; Ocariz, J; Roos, L; Therin, G; Behera, P K; Gladney, L; Guo, Q H; Panetta, J; Biasini, M; Covarelli, R; Pacetti, S; Pioppi, M; Angelini, C; Batignani, G; Bettarini, S; Bucci, F; Calderini, G; Carpinelli, M; Cenci, R; Forti, F; Giorgi, M A; Lusiani, A; Marchiori, G; Morganti, M; Neri, N; Paoloni, E; Rama, M; Rizzo, G; Walsh, J; Haire, M; Judd, D; Wagoner, D E; Biesiada, J; Danielson, N; Elmer, P; Lau, Y P; Lu, C; Olsen, J; Smith, A J S; Telnov, A V; Bellini, F; Cavoto, G; D'Orazio, A; Di Marco, E; Faccini, R; Ferrarotto, F; Ferroni, F; Gaspero, M; Li Gioi, L; Mazzoni, M A; Morganti, S; Piredda, G; Polci, F; Safai Tehrani, F; Voena, C; Schröder, H; Wagner, G; Waldi, R; Adye, T; De Groot, N; Franek, B; Gopal, G P; Olaiya, E O; Wilson, F F; Aleksan, R; Emery, S; Gaidot, A; Ganzhur, S F; Giraud, P-F; Graziani, G; Hamel de Monchenault, G; Kozanecki, W; Legendre, M; London, G W; Mayer, B; Vasseur, G; Yèche, Ch; Zito, M; Purohit, M V; Weidemann, A W; Wilson, J R; Yumiceva, F X; Abe, T; Allen, M T; Aston, D; Bartoldus, R; Berger, N; Boyarski, A M; Buchmueller, O L; Claus, R; Convery, M R; Cristinziani, M; Dingfelder, J C; Dong, D; Dorfan, J; Dujmic, D; Dunwoodie, W; Fan, S; Field, R C; Glanzman, T; Gowdy, S J; Hadig, T; Halyo, V; Hast, C; Hryn'ova, T; Innes, W R; Kelsey, M H; Kim, P; Kocian, M L; Leith, D W G S; Libby, J; Luitz, S; Luth, V; Lynch, H L; Marsiske, H; Messner, R; Muller, D R; O'Grady, C P; Ozcan, V E; Perazzo, A; Perl, M; Ratcliff, B N; Roodman, A; Salnikov, A A; Schindler, R H; Schwiening, J; Snyder, A; Stelzer, J; Su, D; Sullivan, M K; Suzuki, K; Swain, S; Thompson, J M; Va'vra, J; Weaver, M; Weinstein, A J R; Wisniewski, W J; Wittgen, M; Wright, D H; Yarritu, A K; Yi, K; Young, C C; Burchat, P R; Edwards, A J; Majewski, S A; Petersen, B A; Roat, C; Ahmed, M; Ahmed, S; Alam, M S; Ernst, J A; Saeed, M A; Wappler, F R; Zain, S B; Bugg, W; Krishnamurthy, M; Spanier, S M; Eckmann, R; Ritchie, J L; Satpathy, A; Schwitters, R F; Izen, J M; Kitayama, I; Lou, X C; Ye, S; Bianchi, F; Bona, M; Gallo, F; Gamba, D; Bomben, M; Bosisio, L; Cartaro, C; Cossutti, F; Della Ricca, G; Dittongo, S; Grancagnolo, S; Lanceri, L; Vitale, L; Martinez-Vidal, F; Panvini, R S; Banerjee, Sw; Bhuyan, B; Brown, C M; Fortin, D; Hamano, K; Kowalewski, R; Roney, J M; Sobie, R J; Back, J J; Harrison, P F; Latham, T E; Mohanty, G B; Band, H R; Chen, X; Cheng, B; Dasu, S; Datta, M; Eichenbaum, A M; Flood, K T; Graham, M; Hollar, J J; Johnson, J R; Kutter, P E; Li, H; Liu, R; Mellado, B; Mihalyi, A; Pan, Y; Prepost, R; Tan, P; von Wimmersperg-Toeller, J H; Wu, S L; Yu, Z; Neal, H

    2007-05-25

    We present a measurement of the partial branching fractions and mass spectra of the exclusive radiative penguin processes B-->Kpipigamma in the range m(Kpipi)<1.8 GeV/c(2). We reconstruct four final states: K(+)pi(-)pi(+)gamma, K(+)pi(-)pi(0)gamma, K(S)(0)pi(-)pi(+)gamma, and K(S)(0)pi(+)pi(0)gamma, where K(S)(0)-->pi(+)pi(-). Using 232 x 10(6) e(+)e(-)-->BB events recorded by the BABAR experiment at the SLAC PEP-II asymmetric-energy storage ring, we measure the branching fractions B(B(+)-->K(+)pi(-)pi(+)gamma)=[2.95+/-0.13(stat)+/-0.20(syst)] x 10(-5), B(B(0)-->K(+)pi(-)pi(0)gamma)=[4.07+/-0.22(stat)+/-0.31(syst)] x 10(-5), B(B(0)-->K(0)pi(+)pi(-)gamma)=[1.85+/-0.21(stat)+/-0.12(syst)] x 10(-5), and B(B(+)-->K(0)pi(+)pi(0)gamma)=[4.56+/-0.42(stat)+/-0.31(syst)] x 10(-5).

  10. DtaRefinery: a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra datasets

    SciTech Connect

    Petyuk, Vladislav A.; Mayampurath, Anoop M.; Monroe, Matthew E.; Polpitiya, Ashoka D.; Purvine, Samuel O.; Anderson, Gordon A.; Camp, David G.; Smith, Richard D.

    2009-12-16

    Hybrid two-stage mass spectrometers capable of both highly accurate mass measurement and MS/MS fragmentation have become widely available in recent years and have allowed for sig-nificantly better discrimination between true and false MS/MS pep-tide identifications by applying relatively narrow windows for maxi-mum allowable deviations for parent ion mass measurements. To fully gain the advantage of highly accurate parent ion mass meas-urements, it is important to limit systematic mass measurement errors. The DtaRefinery software tool can correct systematic errors in parent ion masses by reading a set of fragmentation spectra, searching for MS/MS peptide identifications, then fitting a model that can estimate systematic errors, and removing them. This results in a new fragmentation spectrum file with updated parent ion masses.

  11. GPQuest: A Spectral Library Matching Algorithm for Site-Specific Assignment of Tandem Mass Spectra to Intact N-glycopeptides.

    PubMed

    Toghi Eshghi, Shadi; Shah, Punit; Yang, Weiming; Li, Xingde; Zhang, Hui

    2015-01-01

    Glycoprotein changes occur in not only protein abundance but also the occupancy of each glycosylation site by different glycoforms during biological or pathological processes. Recent advances in mass spectrometry instrumentation and techniques have facilitated analysis of intact glycopeptides in complex biological samples by allowing the users to generate spectra of intact glycopeptides with glycans attached to each specific glycosylation site. However, assigning these spectra, leading to identification of the glycopeptides, is challenging. Here, we report an algorithm, named GPQuest, for site-specific identification of intact glycopeptides using higher-energy collisional dissociation (HCD) fragmentation of complex samples. In this algorithm, a spectral library of glycosite-containing peptides in the sample was built by analyzing the isolated glycosite-containing peptides using HCD LC-MS/MS. Spectra of intact glycopeptides were selected by using glycan oxonium ions as signature ions for glycopeptide spectra. These oxonium-ion-containing spectra were then compared with the spectral library generated from glycosite-containing peptides, resulting in assignment of each intact glycopeptide MS/MS spectrum to a specific glycosite-containing peptide. The glycan occupying each glycosite was determined by matching the mass difference between the precursor ion of intact glycopeptide and the glycosite-containing peptide to a glycan database. Using GPQuest, we analyzed LC-MS/MS spectra of protein extracts from prostate tumor LNCaP cells. Without enrichment of glycopeptides from global tryptic peptides and at a false discovery rate of 1%, 1008 glycan-containing MS/MS spectra were assigned to 769 unique intact N-linked glycopeptides, representing 344 N-linked glycosites with 57 different N-glycans. Spectral library matching using GPQuest assigns the HCD LC-MS/MS generated spectra of intact glycopeptides in an automated and high-throughput manner. Additionally, spectral library

  12. AUTOMATED DECONVOLUTION OF COMPOSITE MASS SPECTRA OBTAINED WITH AN OPEN-AIR IONIZATIONS SOURCE BASED ON EXACT MASSES AND RELATIVE ISOTIPIC ABUNDANCES

    EPA Science Inventory

    Chemicals dispersed by accidental, deliberate, or weather-related events must be rapidly identified to assess health risks. Mass spectra from high levels of analytes obtained using rapid, open-air ionization by a Direct Analysis in Real Time (DART®) ion source often contain

  13. Real-time quadrupole mass spectrometer analysis of gas in boreholefluid samples acquired using the U-Tube sampling methodology

    SciTech Connect

    Freifeld, Barry M.; Trautz, Robert C.

    2006-01-11

    Sampling of fluids in deep boreholes is challenging becauseof the necessity to minimize external contamination and maintain sampleintegrity during recovery. The U-tube sampling methodology was developedto collect large volume, multiphase samples at in situ pressures. As apermanent or semi-permanent installation, the U-tube can be used forrapidly acquiring multiple samples or it may be installed for long-termmonitoring applications. The U-tube was first deployed in Liberty County,TX to monitor crosswell CO2 injection as part of the Frio CO2sequestration experiment. Analysis of gases (dissolved or separate phase)was performed in the field using a quadrupole mass spectrometer, whichserved as the basis for determining the arrival of the CO2 plume. Thepresence of oxygen and argon in elevated concentrations, along withreduced methane concentration, indicate sample alteration caused by theintroduction of surface fluids during borehole completion. Despiteproducing the well to eliminate non-native fluids, measurementsdemonstrate that contamination persists until the immiscible CO2injection swept formation fluid into the observationwellbore.

  14. Neutral loss of isocyanic acid in peptide CID spectra: a novel diagnostic marker for mass spectrometric identification of protein citrullination.

    PubMed

    Hao, Gang; Wang, Danchen; Gu, Jane; Shen, Qiuying; Gross, Steven S; Wang, Yanming

    2009-04-01

    Protein citrullination is emerging as an important signaling mechanism that modulates a variety of biological processes. This protein modification constitutes only a 1 Da mass shift, and can be readily confused with other common protein modifications that yield an identical mass shift. In an attempt to develop a robust methodology for detection of protein citrullination sites, we analyzed synthetic citrulline-containing peptides by electrospray ionization tandem mass spectrometry. Collision-induced dissociation (CID) spectra revealed abundant neutral loss of 43 Da from citrullinated peptide precursor ions, which was reconciled by elimination of the HNCO moiety (isocyanic acid) from the citrulline ureido group. The elimination occurs readily in multiple charge states of precursor ions and also in b and y ions. HNCO loss in CID spectra provides a novel diagnostic marker for citrullination, and its utility was demonstrated by the discovery of Arg197 as the specific site of citrullination on nucleophosmin upon peptidylarginine deiminase 4 treatment. PMID:19200748

  15. Measurement of Branching Fractions and Mass Spectra of B to K pi pi gamma

    SciTech Connect

    Aubert, B.; Barate, R.; Boutigny, D.; Couderc, F.; Karyotakis, Y.; Lees, J.P.; Poireau, V.; Tisserand, V.; Zghiche, A.; Grauges, E.; Palano, A.; Pappagallo, M.; Pompili, A.; Chen, J.C.; Qi, N.D.; Rong, G.; Wang, P.; Zhu, Y.S.; Eigen, G.; Ofte, I.; Stugu, B. /Bergen U. /LBL, Berkeley /UC, Berkeley /Birmingham U. /Ruhr U., Bochum /Bristol U. /British Columbia U. /Brunel U. /Novosibirsk, IYF /UC, Irvine /UCLA /UC, Riverside /UC, San Diego /UC, Santa Barbara /UC, Santa Cruz /Caltech /Cincinnati U. /Colorado U. /Colorado State U. /Dortmund U. /Dresden, Tech. U. /Ecole Polytechnique /Edinburgh U. /Ferrara U. /INFN, Ferrara /Frascati /Genoa U. /INFN, Genoa /Harvard U. /Heidelberg U. /Imperial Coll., London /Iowa U. /Iowa State U. /Orsay, LAL /LLNL, Livermore /Liverpool U. /Queen Mary, U. of London /Royal Holloway, U. of London /Louisville U. /Manchester U. /Maryland U. /Massachusetts U., Amherst /MIT, LNS /McGill U. /Milan U. /INFN, Milan /Mississippi U. /Montreal U. /Mt. Holyoke Coll. /Naples U. /INFN, Naples /NIKHEF, Amsterdam /Notre Dame U. /Ohio State U. /Oregon U. /INFN, Padua /Padua U. /Paris U., VI-VII /Pennsylvania U. /Perugia U. /INFN, Perugia /Pisa U. /Pisa, Scuola Normale Superiore /INFN, Pisa /Prairie View A-M /Princeton U. /Rome U. /INFN, Rome /Rostock U. /Rutherford /DAPNIA, Saclay /South Carolina U. /SLAC /Stanford U., Phys. Dept. /SUNY, Albany /Tennessee U. /Texas U. /Texas U., Dallas /Turin U. /INFN, Turin /Trieste U. /INFN, Trieste /Valencia U., IFIC /Vanderbilt U. /Victoria U. /Warwick U. /Wisconsin U., Madison /Yale U.

    2005-07-12

    The authors present a measurement of the partial branching fractions and mass spectra of the exclusive radiative penguin processes B {yields} K{pi}{pi}{gamma} in the range m{sub K{pi}{pi}} < 1.8 GeV/c{sup 2}. They reconstruct four final states: K{sup +}{pi}{sup -}{pi}{sup +}{gamma}, K{sup +}{pi}{sup -}{pi}{sup 0}{gamma}, K{sub S}{sup 0}{pi}{sup -}{pi}{sup +}{gamma}, and K{sub S}{sup 0}{pi}{sup +}{pi}{sup 0}{gamma}, where K{sub S}{sup 0} {yields} {pi}{sup +}{pi}{sup -}. Using 232 million e{sup +}e{sup -} {yields} B{bar B} events recorded by the BABAR experiment at the PEP-II asymmetric-energy storage ring, they measure the branching fractions {Beta}(B{sup +} {yields} K{sup +}{pi}{sup -}{pi}{sup +}{gamma}) = (2.95 {+-} 0.13(stat.) {+-} 0.20(syst)) x 10{sup -5}, {Beta}(B{sup 0} {yields} K{sup +}{pi}{sup -}{pi}{sup 0}{gamma}) = (4.07 {+-} 0.22(stat.) {+-} 0.31(syst.)) x 10{sup -5}, {Beta}(B{sup 0} {yields} K{sup 0}{pi}{sup +}{pi}{sup -}{gamma}) = (1.85 {+-} 0.21(stat.) {+-} 0.12(syst.)) x 10{sup -5}, and {Beta}(B{sup +} {yields} K{sup 0}{pi}{sup +}{pi}{sup 0}{gamma}) = (4.56 {+-} 0.42(stat.) {+-} 0.31(syst.)) x 10{sup -5}.

  16. Three-dimensional factorization of size-resolved organic aerosol mass spectra from Mexico City

    NASA Astrophysics Data System (ADS)

    Ulbrich, I. M.; Canagaratna, M. R.; Cubison, M. J.; Zhang, Q.; Ng, N. L.; Aiken, A. C.; Jimenez, J. L.

    2011-07-01

    A size-resolved submicron organic aerosol composition dataset from a high-resolution time-of-flight mass spectrometer (HR-ToF-AMS) collected in Mexico City during the MILAGRO campaign in March 2006 is analyzed using 3-dimensional (3-D) factorization models. A method for estimating the precision of the size-resolved composition data for use with the factorization models is presented here for the first time. Two 3-D models are applied to the dataset. One model is a 3-vector decomposition (PARAFAC model), which assumes that each chemical component has a constant size distribution over all time steps. The second model is a vector-matrix decomposition (Tucker 1 model) that allows a chemical component to have a size distribution that varies in time. To our knowledge, this is the first report of an application of 3-D factorization models to data from fast aerosol instrumentation; it is also the first application of this vector-matrix model to any ambient aerosol dataset. A larger number of degrees of freedom in the vector-matrix model enable fitting real variations in factor size distributions, but also make the model susceptible to fitting noise in the dataset, giving some unphysical results. For this dataset and model, more physical results were obtained by partially constraining the factor mass spectra using a priori information and a new regularization method. We find four factors with each model: hydrocarbon-like organic aerosol (HOA), biomass-burning organic aerosol (BBOA), oxidized organic aerosol (OOA), and a locally occurring organic aerosol (LOA). These four factors have previously been reported from 2-dimensional factor analysis of the high-resolution mass spectral dataset from this study. The size distributions of these four factors are consistent with previous reports for these particle types. Both 3-D models produce useful results, but the vector-matrix model captures real variability in the size distributions that cannot be captured by the 3-vector model. A

  17. Three-dimensional factorization of size-resolved organic aerosol mass spectra from Mexico City

    NASA Astrophysics Data System (ADS)

    Ulbrich, I. M.; Canagaratna, M. R.; Cubison, M. J.; Zhang, Q.; Ng, N. L.; Aiken, A. C.; Jimenez, J. L.

    2012-01-01

    A size-resolved submicron organic aerosol composition dataset from a high-resolution time-of-flight mass spectrometer (HR-ToF-AMS) collected in Mexico City during the MILAGRO campaign in March 2006 is analyzed using 3-dimensional (3-D) factorization models. A method for estimating the precision of the size-resolved composition data for use with the factorization models is presented here for the first time. Two 3-D models are applied to the dataset. One model is a 3-vector decomposition (PARAFAC model), which assumes that each chemical component has a constant size distribution over all time steps. The second model is a vector-matrix decomposition (Tucker 1 model) that allows a chemical component to have a size distribution that varies in time. To our knowledge, this is the first report of an application of 3-D factorization models to data from fast aerosol instrumentation, and the first application of this vector-matrix model to any ambient aerosol dataset. A larger number of degrees of freedom in the vector-matrix model enable fitting real variations in factor size distributions, but also make the model susceptible to fitting noise in the dataset, giving some unphysical results. For this dataset and model, more physically meaningful results were obtained by partially constraining the factor mass spectra using a priori information and a new regularization method. We find four factors with each model: hydrocarbon-like organic aerosol (HOA), biomass-burning organic aerosol (BBOA), oxidized organic aerosol (OOA), and a locally occurring organic aerosol (LOA). These four factors have previously been reported from 2-dimensional factor analysis of the high-resolution mass spectral dataset from this study. The size distributions of these four factors are consistent with previous reports for these particle types. Both 3-D models produce useful results, but the vector-matrix model captures real variability in the size distributions that cannot be captured by the 3-vector

  18. Characterization of signatures from organic compounds in CDA mass spectra of ice particles in Saturn's E-ring

    NASA Astrophysics Data System (ADS)

    Khawaja, Nozair; Postberg, Frank; Reviol, Rene; Srama, Ralf

    2015-04-01

    The major source of ice particles in Saturn's E-ring is Enceladus - a geological active moon of Saturn. Enceladus is emanating ice particles from its fractured south polar terrain (SPT), the so-called "Tiger Stripes". The source of Enceladus activity and many of the ice particles is a subsurface ocean. The Cosmic Dust Analyzer (CDA) onboard the Cassini spacecraft is sampling these icy particles and producing TOF mass spectra of cations of impinging particles [1]. Three compositional types of ice particles have been identified from CDA-mass spectra: (i) pure water ice (Type-1) (ii) organic rich (Type-2) (iii) salt rich (Type-3) [2][3]. These organic rich (Type-2) spectra are particularly abundant in the icy jets of Enceladus as we found out during the Cassini's Enceladus flybys (E17 and E18) in 2012 [4]. We present a compositional analysis of the CDA spectra of these organic rich icy grains sampled in the E ring. We have characterized hundreds of Type-2 spectra of impinging ice particles. These were recorded at different impact velocities causing different molecular fragmentation patterns observed in the mass spectra. We defined 3 typical impact speed intervals: (i) 4-7 km/s (ii) 8-11 km/s and (iii) 12-16km/s. Organic features best observed at slow (4-7 km/s) or at intermediate (8-11 km/s) impact velocity ranges. Several classes of organic rich spectra are identified. Classifying Type-2 spectra are according to their characteristic mass lines of possible organic species. We try to infer the composition of each class of organic rich spectra is inferred by using an experimental setup (IR-FL-MALDI) to simulate the CDA spectra of different compositional types. In the laboratory we have used infrared laser to disperse a micro-beam of a water solution [5]. The laser energy is adjusted to simulate different impact velocities of ice particles on the CDA. Four families of organic compounds including alcohols, fatty acids, amines and aromatic, with varying number of carbon

  19. PHYSICAL PROPERTIES OF YOUNG BROWN DWARFS AND VERY LOW MASS STARS INFERRED FROM HIGH-RESOLUTION MODEL SPECTRA

    SciTech Connect

    Rice, Emily L.; Mclean, Ian S.; Barman, T.; Prato, L.; Kirkpatrick, J. Davy

    2010-01-01

    By comparing near-infrared spectra with atmospheric models, we infer the effective temperature, surface gravity, projected rotational velocity, and radial velocity for 21 very low mass stars and brown dwarfs. The unique sample consists of two sequences in spectral type from M6-M9, one of 5-10 Myr objects and one of >1 Gyr field objects. A third sequence is comprised of only {approx}M6 objects with ages ranging from <1 Myr to >1 Gyr. Spectra were obtained in the J band at medium (R {approx} 2000) and high (R {approx} 20,000) resolutions with NIRSPEC on the Keck II telescope. Synthetic spectra were generated from atmospheric structures calculated with the PHOENIX model atmosphere code. Using multi-dimensional least-squares fitting and Monte Carlo routines we determine the best-fit model parameters for each observed spectrum and note which spectral regions provide consistent results. We identify successes in the reproduction of observed features by atmospheric models, including pressure-broadened K I lines, and investigate deficiencies in the models, particularly missing FeH opacity, that will need to be addressed in order to extend our analysis to cooler objects. The precision that can be obtained for each parameter using medium- and high-resolution near-infrared spectra is estimated and the implications for future studies of very low mass stars and brown dwarfs are discussed.

  20. Suzaku spectra of the neutron-star low-mass X-ray binary 4U 1608-52

    NASA Astrophysics Data System (ADS)

    Lei, Yajuan; Zhang, Haotong; zhang, Yanxia

    2015-08-01

    We present the spectral analysis of the neutron-star low-mass X-ray binary 4U 1608-52 using data from four Suzaku observations in 2010 March. 4U 1608-52 is a transient atoll source, and the analyzed observations contain the “island” and “banana” states, corresponding transitional, and soft states. The spectra are fitted with the hybrid model for the soft states, which consists of two thermal components (a multicolor accretion disk and a single-temperature blackbody) plus a broken power law. The fitting results show that the continuum spectra evolve during the different states. Fe emission line is often detected in low-mass X-ray binary, however, no obviously Fe line is detected in the four observations of 4U 1608-52.

  1. Building an empirical mass spectra library for screening of organic pollutants by ultra-high-pressure liquid chromatography/hybrid quadrupole time-of-flight mass spectrometry.

    PubMed

    Díaz, Ramón; Ibáñez, María; Sancho, Juan V; Hernández, Félix

    2011-01-30

    Hybrid quadrupole time-of-flight mass spectrometry (QTOF MS) has gained wide acceptance in many fields of chemistry, for example, proteomics, metabolomics and small molecule analysis. This has been due to the numerous technological advances made to this mass analyser in recent years. In the environmental field, the instrument has proven to be one of the most powerful approaches for the screening of organic pollutants in different matrices due to its high sensitivity in full acquisition mode and mass accuracy measurements. In the work presented here, the optimum experimental conditions for the creation of an empirical TOF MS spectra library have been evaluated. For this model we have used a QTOF Premier mass spectrometer and investigated its functionalities to obtain the best MS data, mainly in terms of mass accuracy, dynamic range and sensitivity. Different parameters that can affect mass accuracy, such as lock mass, ion abundance, spectral resolution, instrument calibration or matrix effect, have also been carefully evaluated using test compounds (mainly pesticides and antibiotics). The role of ultra-high-pressure liquid chromatography (UHPLC), especially when dealing with complex matrices, has also been tested. In addition to the mass accuracy measurements, this analyser allows the simultaneous acquisition of low and high collision energy spectra. This acquisition mode greatly enhances the reliable identification of detected compounds due to the useful (de)protonated molecule and fragment ion accurate mass information obtained when working in this mode. An in-house empirical spectral library was built for approximately 230 organic pollutants making use of QTOF MS in MS(E) mode. All the information reported in this paper is made available to the readers to facilitate screening and identification of relevant organic pollutants by QTOF MS.

  2. Mass spectra of cyclic ethers formed in the low-temperature oxidation of a series of n-alkanes

    PubMed Central

    Herbinet, Olivier; Bax, Sarah; Glaude, Pierre-Alexandre; Carré, Vincent; Battin-Leclerc, Frédérique

    2013-01-01

    Cyclic ethers are important intermediate species formed during the low-temperature oxidation of hydrocarbons. Along with ketones and aldehydes, they could consequently represent a significant part of the heavy oxygenated pollutants observed in the exhaust gas of engines. Apart a few of them such as ethylene oxide and tetrahydrofuran, cyclic ethers have not been much studied and very few of them are available for calibration and identification. Electron impact mass spectra are available for very few of them, making their detection in the exhaust emissions of combustion processes very difficult. The main goal of this study was to complete the existing set of mass spectra for this class of molecules. Thus cyclic ethers have been analyzed in the exhaust gases of a jet-stirred reactor in which the low-temperature oxidation of a series of n-alkanes was taking place. Analyzes were performed by gas chromatography coupled to mass spectrometry and to MS/MS. The second goal of this study was to derive some rules for the fragmentation of cyclic ethers in electron impact mass spectrometry and allow the identification of these species when no mass spectrum is available. PMID:24092947

  3. Mass spectra of cyclic ethers formed in the low-temperature oxidation of a series of n-alkanes.

    PubMed

    Herbinet, Olivier; Bax, Sarah; Glaude, Pierre-Alexandre; Carré, Vincent; Battin-Leclerc, Frédérique

    2011-02-01

    Cyclic ethers are important intermediate species formed during the low-temperature oxidation of hydrocarbons. Along with ketones and aldehydes, they could consequently represent a significant part of the heavy oxygenated pollutants observed in the exhaust gas of engines. Apart a few of them such as ethylene oxide and tetrahydrofuran, cyclic ethers have not been much studied and very few of them are available for calibration and identification. Electron impact mass spectra are available for very few of them, making their detection in the exhaust emissions of combustion processes very difficult. The main goal of this study was to complete the existing set of mass spectra for this class of molecules. Thus cyclic ethers have been analyzed in the exhaust gases of a jet-stirred reactor in which the low-temperature oxidation of a series of n-alkanes was taking place. Analyzes were performed by gas chromatography coupled to mass spectrometry and to MS/MS. The second goal of this study was to derive some rules for the fragmentation of cyclic ethers in electron impact mass spectrometry and allow the identification of these species when no mass spectrum is available. PMID:24092947

  4. THE MASS-METALLICITY RELATION WITH THE DIRECT METHOD ON STACKED SPECTRA OF SDSS GALAXIES

    SciTech Connect

    Andrews, Brett H.; Martini, Paul

    2013-03-10

    The relation between galaxy stellar mass and gas-phase metallicity is a sensitive diagnostic of the main processes that drive galaxy evolution, namely cosmological gas inflow, metal production in stars, and gas outflow via galactic winds. We employed the direct method to measure the metallicities of {approx}200,000 star-forming galaxies from the Sloan Digital Sky Survey that were stacked in bins of (1) stellar mass and (2) both stellar mass and star formation rate (SFR) to significantly enhance the signal-to-noise ratio of the weak [O III] {lambda}4363 and [O II] {lambda}{lambda}7320, 7330 auroral lines required to apply the direct method. These metallicity measurements span three decades in stellar mass from log(M{sub *}/M{sub Sun }) = 7.4-10.5, which allows the direct method mass-metallicity relation to simultaneously capture the high-mass turnover and extend a full decade lower in mass than previous studies that employed more uncertain strong line methods. The direct method mass-metallicity relation rises steeply at low mass (O/H {proportional_to} M{sub *} {sup 1/2}) until it turns over at log(M{sub *}/M{sub Sun }) = 8.9 and asymptotes to 12 + log(O/H) = 8.8 at high mass. The direct method mass-metallicity relation has a steeper slope, a lower turnover mass, and a factor of two to three greater dependence on SFR than strong line mass-metallicity relations. Furthermore, the SFR-dependence appears monotonic with stellar mass, unlike strong line mass-metallicity relations. We also measure the N/O abundance ratio, an important tracer of star formation history, and find the clear signature of primary and secondary nitrogen enrichment. N/O correlates tightly with oxygen abundance, and even more so with stellar mass.

  5. Approaches towards the automated interpretation and prediction of electrospray tandem mass spectra of non-peptidic combinatorial compounds.

    PubMed

    Klagkou, Katerina; Pullen, Frank; Harrison, Mark; Organ, Andy; Firth, Alistair; Langley, G John

    2003-01-01

    Combinatorial chemistry is widely used within the pharmaceutical industry as a means of rapid identification of potential drugs. With the growth of combinatorial libraries, mass spectrometry (MS) became the key analytical technique because of its speed of analysis, sensitivity, accuracy and ability to be coupled with other analytical techniques. In the majority of cases, electrospray mass spectrometry (ES-MS) has become the default ionisation technique. However, due to the absence of fragment ions in the resulting spectra, tandem mass spectrometry (MS/MS) is required to provide structural information for the identification of an unknown analyte. This work discusses the first steps of an investigation into the fragmentation pathways taking place in electrospray tandem mass spectrometry. The ultimate goal for this project is to set general fragmentation rules for non-peptidic, pharmaceutical, combinatorial compounds. As an aid, an artificial intelligence (AI) software package is used to facilitate interpretation of the spectra. This initial study has focused on determining the fragmentation rules for some classes of compound types that fit the remit as outlined above. Based on studies carried out on several combinatorial libraries of these compounds, it was established that different classes of drug molecules follow unique fragmentation pathways. In addition to these general observations, the specific ionisation processes and the fragmentation pathways involved in the electrospray mass spectra of these systems were explored. The ultimate goal will be to incorporate our findings into the computer program and allow identification of an unknown, non-peptidic compound following insertion of its ES-MS/MS spectrum into the AI package. The work herein demonstrates the potential benefit of such an approach in addressing the issue of high-throughput, automated MS/MS data interpretation.

  6. Splitting mass spectra and muon g - 2 in Higgs-anomaly mediation

    NASA Astrophysics Data System (ADS)

    Yin, Wen; Yokozaki, Norimi

    2016-11-01

    We propose a scenario where only the Higgs multiplets have direct couplings to a supersymmetry (SUSY) breaking sector. The standard model matter multiplets as well as the gauge multiples are sequestered from the SUSY breaking sector; therefore, their masses arise via anomaly mediation at the high energy scale with a gravitino mass of ∼ 100TeV. Due to renormalization group running effects from the Higgs soft masses, the masses of the third generation sfermions become O (10)TeV at the low energy scale, while the first and second generation sfermion masses are O (0.1- 1)TeV, avoiding the tachyonic slepton problem and flavor changing neutral current problem. With the splitting mass spectrum, the muon g - 2 anomaly is explained consistently with the observed Higgs boson mass of 125 GeV. Moreover, the third generation Yukawa couplings are expected to be unified in some regions. New contributions to the Higgs boson mass: if there is an additional contribution to the Higgs boson mass, the SUSY particles are not necessarily heavy. In this case, the anomaly of the muon g - 2 is explained by the contributions from the fairly light SUSY particles. For instance, SUSY models with vector-like matter multiplets [14-17], the large trilinear coupling of the stop [18,19], or an extra gauge interaction [20] can accommodate both the observed Higgs boson mass and muon g - 2 anomaly.

  7. Galaxy And Mass Assembly (GAMA) blended spectra catalogue: strong galaxy-galaxy lens and occulting galaxy pair candidates

    NASA Astrophysics Data System (ADS)

    Holwerda, B. W.; Baldry, I. K.; Alpaslan, M.; Bauer, A.; Bland-Hawthorn, J.; Brough, S.; Brown, M. J. I.; Cluver, M. E.; Conselice, C.; Driver, S. P.; Hopkins, A. M.; Jones, D. H.; López-Sánchez, Á. R.; Loveday, J.; Meyer, M. J.; Moffett, A.

    2015-06-01

    We present the catalogue of blended galaxy spectra from the Galaxy And Mass Assembly (GAMA) survey. These are cases where light from two galaxies are significantly detected in a single GAMA fibre. Galaxy pairs identified from their blended spectrum fall into two principal classes: they are either strong lenses, a passive galaxy lensing an emission-line galaxy; or occulting galaxies, serendipitous overlaps of two galaxies, of any type. Blended spectra can thus be used to reliably identify strong lenses for follow-up observations (high-resolution imaging) and occulting pairs, especially those that are a late-type partly obscuring an early-type galaxy which are of interest for the study of dust content of spiral and irregular galaxies. The GAMA survey setup and its AUTOZ automated redshift determination were used to identify candidate blended galaxy spectra from the cross-correlation peaks. We identify 280 blended spectra with a minimum velocity separation of 600 km s-1, of which 104 are lens pair candidates, 71 emission-line-passive pairs, 78 are pairs of emission-line galaxies and 27 are pairs of galaxies with passive spectra. We have visually inspected the candidates in the Sloan Digital Sky Survey (SDSS) and Kilo Degree Survey (KiDS) images. Many blended objects are ellipticals with blue fuzz (Ef in our classification). These latter `Ef' classifications are candidates for possible strong lenses, massive ellipticals with an emission-line galaxy in one or more lensed images. The GAMA lens and occulting galaxy candidate samples are similar in size to those identified in the entire SDSS. This blended spectrum sample stands as a testament of the power of this highly complete, second-largest spectroscopic survey in existence and offers the possibility to expand e.g. strong gravitational lens surveys.

  8. AUTOMATED ELEMENTAL COMPOSITION DETERMINATION AND CORRELATION OF PRECURSOR WITH PRODUCT IONS BASED ON ORTHOGONAL ACCELERATION, TIME-OF-FLIGHT MASS SPECTRA

    EPA Science Inventory

    For more than a decade in our laboratory, elemental compositions of ions in mass spectra havebeen routinely determined by measuring exact masses and relative isotopic abundances of ions in isotopicclusters using a GC coupled to a double focusing mass spectrometer.1 HPLC interfac...

  9. Proteomics of Soil and Sediment: Protein Identification by De Novo Sequencing of Mass Spectra Complements Traditional Database Searching

    NASA Astrophysics Data System (ADS)

    Miller, S.; Rizzo, A. I.; Waldbauer, J.

    2014-12-01

    Proteomics has the potential to elucidate the metabolic pathways and taxa responsible for in situ biogeochemical transformations. However, low rates of protein identification from high resolution mass spectra have been a barrier to the development of proteomics in complex environmental samples. Much of the difficulty lies in the computational challenge of linking mass spectra to their corresponding proteins. Traditional database search methods for matching peptide sequences to mass spectra are often inadequate due to the complexity of environmental proteomes and the large database search space, as we demonstrate with soil and sediment proteomes generated via a range of extraction methods. One alternative to traditional database searching is de novo sequencing, which identifies peptide sequences without the need for a database. BLAST can then be used to match de novo sequences to similar genetic sequences. Assigning confidence to putative identifications has been one hurdle for the implementation of de novo sequencing. We found that accurate de novo sequences can be screened by quality score and length. Screening criteria are verified by comparing the results of de novo sequencing and traditional database searching for well-characterized proteomes from simple biological systems. The BLAST hits of screened sequences are interrogated for taxonomic and functional information. We applied de novo sequencing to organic topsoil and marine sediment proteomes. Peak-rich proteomes, which can result from various extraction techniques, yield thousands of high-confidence protein identifications, an improvement over previous proteomic studies of soil and sediment. User-friendly software tools for de novo metaproteomics analysis have been developed. This "De Novo Analysis" Pipeline is also a faster method of data analysis than constructing a tailored sequence database for traditional database searching.

  10. Proteomics of Soil and Sediment: Protein Identification by De Novo Sequencing of Mass Spectra Complements Traditional Database Searching

    NASA Astrophysics Data System (ADS)

    Miller, S.; Rizzo, A. I.; Waldbauer, J.

    2015-12-01

    Proteomics has the potential to elucidate the metabolic pathways and taxa responsible for in situ biogeochemical transformations. However, low rates of protein identification from high resolution mass spectra have been a barrier to the development of proteomics in complex environmental samples. Much of the difficulty lies in the computational challenge of linking mass spectra to their corresponding proteins. Traditional database search methods for matching peptide sequences to mass spectra are often inadequate due to the complexity of environmental proteomes and the large database search space, as we demonstrate with soil and sediment proteomes generated via a range of extraction methods. One alternative to traditional database searching is de novo sequencing, which identifies peptide sequences without the need for a database. BLAST can then be used to match de novo sequences to similar genetic sequences. Assigning confidence to putative identifications has been one hurdle for the implementation of de novo sequencing. We found that accurate de novo sequences can be screened by quality score and length. Screening criteria are verified by comparing the results of de novo sequencing and traditional database searching for well-characterized proteomes from simple biological systems. The BLAST hits of screened sequences are interrogated for taxonomic and functional information. We applied de novo sequencing to organic topsoil and marine sediment proteomes. Peak-rich proteomes, which can result from various extraction techniques, yield thousands of high-confidence protein identifications, an improvement over previous proteomic studies of soil and sediment. User-friendly software tools for de novo metaproteomics analysis have been developed. This "De Novo Analysis" Pipeline is also a faster method of data analysis than constructing a tailored sequence database for traditional database searching.

  11. Evolved Late-Type Star FUV Spectra: Mass Loss and Fluorescence

    NASA Technical Reports Server (NTRS)

    Harper, Graham M.

    2005-01-01

    This proposal was for a detailed analysis of the far ultraviolet (FUV) photoionizing radiation that provides crucial input physics for mass loss studies, e.g., observations of the flux below 10448, allow us to constrain the Ca II/Ca III balance and make significant progress beyond previous optical studies on stellar mass loss and circumstellar photochemistry. Our targets selection provided good spectral-type coverage required to help unravel the Ca II/Ca III balance as the mass-loss rates increase by over three orders of magnitude from K5 III to M5 III. We also explored the relationship between the FUV radiation field and other UV diagnostics to allow us to empirically estimate the FUV radiation field for the vast majority of stars which are too faint to be observed with FUSE, and to improve upon their uncertain mass-loss rates.

  12. Comparison between mass spectra of individual organic particles generated by UV laser ablation and in the IR/UV two-step mode

    NASA Astrophysics Data System (ADS)

    Zelenyuk, Alla; Yang, Juan; Imre, Dan

    2009-04-01

    In ablation-based single particle mass spectrometry it is common to find that the mass spectra of particles with identical compositions exhibit significant particle-to-particle fluctuations and high degree of fragmentation. This is particularly true when it comes to particles containing organic compounds. At laser fluence that is sufficient to ionize sulfates, mass spectra of the identical organic particles are classified into multitude of classes, some of which are indistinguishable from elemental carbon. In contrast, the individual particle mass spectra generated in two-step mode, in which an IR laser pulse is used to evaporate the semivolatile particle components and a time delayed UV laser pulse is used to ionize the evaporating plume, exhibit greatly diminished particle-to-particle fluctuations and significantly improved mass spectral quality. Since individual particle mass spectra must first be classified and only then can be averaged and analyzed, the IR/UV mode greatly improves the capability to properly quantify particle compositions. We present an experimental investigation of the properties and behavior of individual particle mass spectra of organic particles that are generated by ablation and in the two-step mode as function of UV laser fluence and the delay between the two lasers. The study shows that the two-step mode yields highly reproducible mass spectra that contain sufficient detail to allow molecular identification. In addition it produces significantly higher mass spectral intensities that are linearly related to the mass of organics in the particles. In contrast, ablation generated mass spectra were found to exhibit high degree of fragmentation and large particle-to-particle fluctuations.

  13. Synthesis of nanoparticles in helium droplets—A characterization comparing mass-spectra and electron microscopy data

    SciTech Connect

    Thaler, Philipp; Volk, Alexander; Lackner, Florian; Steurer, Johannes; Schnedlitz, Martin; Ernst, Wolfgang E.; Knez, Daniel; Haberfehlner, Georg

    2015-10-07

    Micrometer sized helium droplets provide an extraordinary environment for the growth of nanoparticles. The method promises great potential for the preparation of core-shell particles as well as one-dimensional nanostructures, which agglomerate along quantum vortices, without involving solvents, ligands, or additives. Using a new apparatus, which enables us to record mass spectra of heavy dopant clusters (>10{sup 4} amu) and to produce samples for transmission electron microscopy simultaneously, we synthesize bare and bimetallic nanoparticles consisting of various materials (Au, Ni, Cr, and Ag). We present a systematical study of the growth process of clusters and nanoparticles inside the helium droplets, which can be described with a simple theoretical model.

  14. DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

    PubMed

    Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G; Martens, Lennart; Vaudel, Marc; Barsnes, Harald

    2014-02-01

    De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .

  15. Dielectron Mass Spectra in square root of sNN = 200 GeV Copper plus Copper Collisions at PHENIX

    NASA Astrophysics Data System (ADS)

    Campbell, Sarah Catherine

    The dielectron mass spectrum consists of light vector meson decays, correlated heavy quark contributions and decays from other hadronic and photonic sources. Thermal radiation and modifications to the light vector mesons may provide additional signals at low masses above known hadronic sources. The PHENIX sNN = 200 GeV Au+Au and Cu+Cu analyses have measured a centrality dependent excess in the the low mass region between 0.15 GeV/c 2 and 0.75 GeV/c2. Between the φ and the J/ψ, in the intermediate mass range, the correlated heavy quark decays are the primary dielectron source; direct photons may augment this region as well. The Cu+Cu system is sensitive to the onset of the dielectron excess. By studying the Cu+Cu mass spectra and yields as a function of pair pT and collision centrality we obtain further understanding of its behavior. Comparisons to the PHENIX Au+Au and p+p measurements an extrapolations from theory are presented.

  16. Mass spectra of heavy-light mesons in heavy hadron chiral perturbation theory

    NASA Astrophysics Data System (ADS)

    Alhakami, Mohammad H.

    2016-05-01

    We study the masses of the low-lying charm and bottom mesons within the framework of heavy hadron chiral perturbation theory (HHChPT). We work to third order in the chiral expansion, where meson loops contribute. In contrast to previous approaches, we use physical meson masses in evaluating these loops. This ensures that their imaginary parts are consistent with the observed widths of the D mesons. The lowest odd- and even-parity, strange and nonstrange charm mesons provide enough constraints to determine only certain linear combinations of the low-energy constants in the effective Lagrangian. We comment on how lattice QCD could provide further information to disentangle these constants. Then, we use the results from the charm sector to predict the spectrum of odd and even parity of the bottom mesons. The predicted masses from our theory are in good agreement with experimentally measured masses for the case of the odd-parity sector. For the even-parity sector, the B -meson states have not yet been observed; thus, our results provide useful information for experimentalists investigating such states. The near degeneracy of nonstrange and strange scalar B mesons is confirmed in our predictions using HHChPT. We show why previous approaches of using HHChPT in studying the mass degeneracy in the scalar states of charm and bottom meson sectors gave unsatisfactory results.

  17. BRIGHT RAY-LIKE FEATURES IN THE AFTERMATH OF CORONAL MASS EJECTIONS: WHITE LIGHT VERSUS ULTRAVIOLET SPECTRA

    SciTech Connect

    Ciaravella, A.; Webb, D. F.; Giordano, S.; Raymond, J. C.

    2013-03-20

    Current sheets (CSs) are important signatures of magnetic reconnection in the eruption of confined solar magnetic structures. Models of coronal mass ejections (CMEs) involve formation of a CS connecting the ejected flux rope with the post-eruption magnetic loops. CSs have been identified in white light (WL) images of CMEs as narrow rays trailing the outward moving CME core, and in ultraviolet spectra as narrow bright features emitting the [Fe XVIII] line. In this work, samples of rays detected in WL images or in ultraviolet spectra have been analyzed. Temperatures, widths, and line intensities of the rays have been measured, and their correlation to the CME properties has been studied. The samples show a wide range of temperatures with hot, coronal, and cool rays. In some cases, the UV spectra support the identification of rays as CSs, but they show that some WL rays are cool material from the CME core. In many cases, both hot and cool material are present, but offset from each other along the Ultraviolet Coronagraph Spectrometer slit. We find that about 18% of the WL rays show very hot gas consistent with the CS interpretation, while about 23% show cold gas that we attribute to cool prominence material draining back from the CME core. The remaining events have ordinary coronal temperatures, perhaps because they have relaxed back to a quiescent state.

  18. CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra

    PubMed Central

    Allen, Felicity; Pon, Allison; Wilson, Michael; Greiner, Russ; Wishart, David

    2014-01-01

    CFM-ID is a web server supporting three tasks associated with the interpretation of tandem mass spectra (MS/MS) for the purpose of automated metabolite identification: annotation of the peaks in a spectrum for a known chemical structure; prediction of spectra for a given chemical structure and putative metabolite identification—a predicted ranking of possible candidate structures for a target spectrum. The algorithms used for these tasks are based on Competitive Fragmentation Modeling (CFM), a recently introduced probabilistic generative model for the MS/MS fragmentation process that uses machine learning techniques to learn its parameters from data. These algorithms have been extensively tested on multiple datasets and have been shown to out-perform existing methods such as MetFrag and FingerId. This web server provides a simple interface for using these algorithms and a graphical display of the resulting annotations, spectra and structures. CFM-ID is made freely available at http://cfmid.wishartlab.com. PMID:24895432

  19. Mass spectra and leptonic decay widths of heavy quarkonia by using psi function

    NASA Astrophysics Data System (ADS)

    Abou-Salem, L. I.

    2004-10-01

    In this study, a non-relativistic two-body wave equation is used to describe the properties of heavy quark-antiquark systems with a potential proportional to the psgr-function. The wave equation is transformed into a true eigenvalue equation and solved numerically. Both the resonance masses and the leptonic decay widths of c\\bar c and b\\skew{-5}\\barb mesons are calculated. The obtained results showed that the quark-antiquark interaction in these systems could be described adequately by using this simple potential form which contains one adjustable parameter besides the quark masses.

  20. Mass spectra of neutral particles released during electrical breakdown of thin polymer films

    NASA Technical Reports Server (NTRS)

    Kendall, B. R. F.

    1985-01-01

    A special type of time-of-flight mass spectrometer triggered from the breakdown event was developed to study the composition of the neutral particle flux released during the electrical breakdown of polymer films problem. Charge is fed onto a metal-backed polymer surface by a movable smooth platinum contact. A slowly increasing potential from a high-impedance source is applied to the contact until breakdown occurs. The breakdown characteristics is made similar to those produced by an electron beam charging system operating at similar potentials. The apparatus showed that intense instantaneous fluxes of neutral particles are released from the sites of breakdown events. For Teflon FEP films of 50 and 75 microns thickness the material released consists almost entirely of fluorocarbon fragments, some of them having masses greater than 350 atomic mass units amu, while the material released from a 50 micron Kapton film consists mainly of light hydrocarbons with masses at or below 44 amu, with additional carbon monoxide and carbon dioxide. The apparatus is modified to allow electron beam charging of the samples.

  1. Automated charge state determination of complex isotope-resolved mass spectra by peak-target Fourier transform.

    PubMed

    Chen, Li; Yap, Yee Leng

    2008-01-01

    This study describes a new algorithm for charge state determination of complex isotope-resolved mass spectra. This algorithm is based on peak-target Fourier transform (PTFT) of isotope packets. It is modified from the widely used Fourier transform method because Fourier transform may give ambiguous charge state assignment for low signal-to-noise ratio (S/N) or overlapping isotopic clusters. The PTFT algorithm applies a novel "folding" strategy to enhance peaks that are symmetrically spaced about the targeted peak before applying the FT. The "folding" strategy multiplies each point to the high-m/z side of the targeted peak by its counterpart on the low-m/z side. A Fourier transform of this "folded" spectrum is thus simplified, emphasizing the charge state of the "chosen" ion, whereas ions of other charge states contribute less to the transformed data. An intensity-dependent technique is also proposed for charge state determination from frequency signals. The performance of PTFT is demonstrated using experimental electrospray ionization Fourier transform ion cyclotron resonance mass spectra. The results show that PTFT is robust for charge state determination of low S/N and overlapping isotopic clusters, and also useful for manual verification of potential hidden isotopic clusters that may be missed by the current analysis algorithms, i.e., AID-MS or THRASH.

  2. Effect of impurities on the matrix-assisted laser desorption mass spectra of single-stranded oligodeoxynucleotides.

    PubMed

    Shaler, T A; Wickham, J N; Sannes, K A; Wu, K J; Becker, C H

    1996-02-01

    The effect of impurities on the analysis of single-stranded DNA oligomers by the technique of matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry has been studied using the matrix 3-hydroxypicolinic acid and 355-nm pulsed light. By mixing the DNA oligomers with different concentrations of impurities and recording mass spectra, limits are set on the tolerable level of a given impurity in a sample. The tolerance limits for sodium chloride, potassium chloride, sodium acetate, sodium fluoride, sodium dodecyl sulfate (SDS), and manganese(II) chloride were found to be approximately 10(-2) M. It was found that magnesium salts degraded the mass spectrum at much lower levels of 10(-4) M. The organic compounds tris(hydroxymethyl)aminomethane (Tris), urea, dithiothreitol (DTT), glycerol, and ethylenediaminetetraacetic acid (EDTA), when present as its ammonium salt, were tolerable at concentrations into the range of 0.25-0.5 M, while the organic polyamine compound spermine substantially degraded the mass spectrum at concentrations above 10(-2) M. When comparing these results for DNA analysis with previously reported limits for protein analysis, large differences are seen for some of the impurities tested. PMID:8712365

  3. A technique for obtaining matrix-assisted laser desorption/ionization time-of-flight mass spectra of poorly soluble and insoluble aromatic polyamides.

    PubMed

    Gies, Anthony P; Nonidez, William K

    2004-04-01

    Wet grinding methods for obtaining matrix-assisted laser desorption/ionization time-of-flight mass spectra of poorly soluble and insoluble low molecular mass oligomers (<4600 Da) of Nomex and Kevlar are described. Optimum conditions for sample preparation are given along with a detailed analysis of the spectra obtained. Two matrix materials were employed in this analysis, 1,8-dihydroxyanthrone (dithranol) and 3-aminoquinoline with potassium trifluoroacetate used as the cationizing agent. The spectra obtained in this study are sensitive to the matrix, molar mixing ratios of matrix/polymer/cationizing agent, and the sample preparation method. PMID:15053662

  4. Fitting of Hadron Mass Spectra and Contributions to Perturbation Theory of Conformal Quantum Field Theory

    NASA Astrophysics Data System (ADS)

    Luna Acosta, German Aurelio

    The masses of observed hadrons are fitted according to the kinematic predictions of Conformal Relativity. The hypothesis gives a remarkably good fit. The isospin SU(2) gauge invariant Lagrangian L(,(pi)NN)(x,(lamda)) is used in the calculation of d(sigma)/d(OMEGA) to 2nd-order Feynman graphs for simplified models of (pi)N(--->)(pi)N. The resulting infinite mass sums over the nucleon (Conformal) families are done via the Generalized-Sommerfeld-Watson Transform Theorem. Even though the models are too simple to be realistic, they indicate that if (DELTA)-internal lines were to be included, 2nd-order Feynman graphs may reproduce the experimental data qualitatively. The energy -dependence of the propagator and couplings in Conformal QFT is different from that of ordinary QFT. Suggestions for further work are made in the areas of ultra-violet divergences and OPEC calculations.

  5. Fingerprint spectra in Laser Microprobe Mass Analysis of titanium oxides of different stoichiometry

    NASA Astrophysics Data System (ADS)

    Michiels, Eric; Gijbels, Renaat

    Micrometric particles of powdered titanium oxides of different stoichiometry (TiO 2, Ti 2O 3 and TiO) are examined by Laser Microprobe Mass Analysis (LAMMA). The stoichiometry of the compound can be correlated with the relative intensity distributions of the (positive or negative) cluster and atomic ions. Application of the "valence model" yields similar conclusions. Variations in laser energy density and in ion lens potential also effect the ion intensity distributions.

  6. SELDI-TOF mass spectra: a view on sources of variation.

    PubMed

    Dijkstra, Martijn; Vonk, Roel J; Jansen, Ritsert C

    2007-02-15

    Adequate interpretation of mass spectrometry data can yield valuable biomarkers. However, spectrum interpretation is a complicated task. This paper reviews the various factors that determine a sample's spectrum and demonstrates the role of these factors in the interpretation process. We derive a simulation model that adequately predicts the expected spectrum based on known sample content and, in the reverse mode, obtain an analysis model that adequately fits an observed spectrum based on the hypothesized sources of variation. PMID:17118720

  7. Ant colony optimization for biomarker identification from MALDI-TOF mass spectra.

    PubMed

    Ressom, Habtom W; Varghese, Rency S; Orvisky, Eduard; Drake, Steven K; Hortin, Glen L; Abdel-Hamid, Mohamed; Loffredo, Christopher A; Goldman, Radoslav

    2006-01-01

    We present a novel method that combines ant colony optimization with support vector machines (ACO-SVM) to select candidate biomarkers from MALDI-TOF serum profiles of hepatocellular carcinoma (HCC) patients and matched controls. The method identified relevant mass points that achieve high sensitivity and specificity in distinguishing HCC patients from healthy individuals. The results indicate that the MALDI-TOF technology could provide the means to discover novel biomarkers for HCC. PMID:17946638

  8. Ant colony optimization for biomarker identification from MALDI-TOF mass spectra.

    PubMed

    Ressom, Habtom W; Varghese, Rency S; Orvisky, Eduard; Drake, Steven K; Hortin, Glen L; Abdel-Hamid, Mohamed; Loffredo, Christopher A; Goldman, Radoslav

    2006-01-01

    We present a novel method that combines ant colony optimization with support vector machines (ACO-SVM) to select candidate biomarkers from MALDI-TOF serum profiles of hepatocellular carcinoma (HCC) patients and matched controls. The method identified relevant mass points that achieve high sensitivity and specificity in distinguishing HCC patients from healthy individuals. The results indicate that the MALDI-TOF technology could provide the means to discover novel biomarkers for HCC.

  9. Solid CO2 in low-mass young stellar objects. Comparison between Spitzer and laboratory spectra

    NASA Astrophysics Data System (ADS)

    Ioppolo, S.; Sangiorgio, I.; Baratta, G. A.; Palumbo, M. E.

    2013-06-01

    Context. Solid interstellar CO2 is an abundant component of ice dust mantles. Its ubiquity towards quiescent molecular clouds, as well as protostellar envelopes, has recently been confirmed by the IRS (InfraRed Spectrograph) aboard the Spitzer Space Telescope. Although it has been shown that CO2 cannot be efficiently formed in the gas phase, the CO2 surface formation pathway is still unclear. To date several CO2 surface formation mechanisms induced by energetic (e.g., UV photolysis and cosmic ray irradiation) and non-energetic (e.g., cold atom addition) input have been proposed. Aims: Our aim is to investigate the contribution of cosmic ray irradiation to the formation of CO2 in different regions of the interstellar medium (ISM). To achieve this goal we compared quantitatively laboratory data with the CO2 bending mode band profile observed towards several young stellar objects (YSOs) and a field star by the Spitzer Space Telescope. Methods: All the experiments presented here were performed at the Laboratory for Experimental Astrophysics in Catania (Italy). The interstellar relevant samples were all irradiated with fast ions (30-200 keV) and subsequently annealed in a stainless steel high vacuum chamber (P < 10-7 mbar). Chemical and structural modifications of the ice samples were monitored by means of infrared spectroscopy. Laboratory spectra were then used to fit some thirty observational spectra. Results: A qualitative analysis shows that a good fit can be obtained with a minimum of two components. The choice of the laboratory components is based on the chemical-physical condition of each source. A quantitative analysis of the sources with known visual extinction (AV) and methanol abundances highlights that the solid carbon dioxide can be efficiently and abundantly formed after ion irradiation of interstellar ices in all the selected YSOs in a time compatible with cloud lifetimes (3 × 107 years). Only in the case of field stars can the expected CO2 column

  10. ULTRAVIOLET EMISSION-LINE CORRELATIONS IN HST/COS SPECTRA OF ACTIVE GALACTIC NUCLEI: SINGLE-EPOCH BLACK HOLE MASSES

    SciTech Connect

    Tilton, Evan M.; Shull, J. Michael E-mail: michael.shull@colorado.edu

    2013-09-01

    Effective methods of measuring supermassive black hole masses in active galactic nuclei (AGNs) are of critical importance to studies of galaxy evolution. While there has been much success in obtaining masses through reverberation mapping, the extensive observing time required by this method has limited the practicality of applying it to large samples at a variety of redshifts. This limitation highlights the need to estimate these masses using single-epoch spectroscopy of ultraviolet (UV) emission lines. We use UV spectra of 44 AGNs from HST/COS, the International Ultraviolet Explorer, and the Far Ultraviolet Spectroscopic Explorer of the C IV {lambda}1549, O VI {lambda}1035, O III] {lambda}1664, He II {lambda}1640, C II {lambda}1335, and Mg II {lambda}2800 emission lines and explore their potential as tracers of the broad-line region and supermassive black hole mass. The higher signal-to-noise ratio and better spectral resolution of the Cosmic Origins Spectrograph (COS) on the Hubble Space Telescope (HST) resolve AGN intrinsic absorption and produce more accurate line widths. From these, we test the viability of mass-scaling relationships based on line widths and luminosities and carry out a principal component analysis based on line luminosities, widths, skewness, and kurtosis. At L{sub 1450} {<=} 10{sup 45} erg s{sup -1}, the UV line luminosities correlate well with H{beta}, as does the 1450 A continuum luminosity. We find that C IV, O VI, and Mg II can be used as reasonably accurate estimators of AGN black hole masses, while He II and C II are uncorrelated.

  11. Real time three-dimensional echocardiography for quantification of ventricular volumes, mass, and function in children with congenital and acquired heart diseases.

    PubMed

    Balluz, Rula; Liu, Liwen; Zhou, Xiaodong; Ge, Shuping

    2013-04-01

    Quantitative measurement of left ventricular (LV) volumes, mass, and function is one of the most common and important indications for echocardiography. These measurements are among the most powerful tools for diagnosis and prognosis of congenital and acquired heart diseases and for assessment of medical, percutaneous, and surgical interventions. Awareness is also growing of the importance of right ventricular (RV) volume, mass, and function in many cardiopulmonary diseases. Furthermore, there are challenges and opportunities to measure the volume, mass, and function of complex chambers such as the left atrium, right atrium, and the univentricular heart. As echocardiography continues to be the imaging modality of choice for these measurements, the strengths and limitations of M-mode, two-dimensional (2D), and recently three-dimensional (3D) echocardiographic (3DE) methodologies for accurate and reproducible measurement of these indices have been extensively investigated for congenital and acquired heart diseases. Evidence suggests that 3DE provides improved accuracy and reproducibility over 2D methods for measurement of LV volume and function calculation in adults and in children. Data have accumulated on the utility of 3DE for measuring chamber volumes and function for the RV and for the single ventricle, which may become more widely used in clinical and research arenas in the future. Finally, new advanced modes of analysis such as 3D strain and synchrony analysis by 3DE are promising methodologies that warrant further investigation.

  12. Nucleon, Delta and Omega excited state spectra at three pion mass values

    SciTech Connect

    John Bulava, Robert G. Edwards, Balint Joo, David G. Richards, Eric Engelson, Huey-Wen Lin, Colin Morningstar, Stephen J. Wallace

    2010-06-01

    The energies of the excited states of the Nucleon, Delta and Omega are computed in lattice QCD, using two light quarks and one strange quark on anisotropic lattices. The calculations are performed at three values of the pion mass: 392(4), 438(3) and 521(3) MeV. We employ the variational method with a basis of about ten interpolating operators enabling six energies to be distinguished clearly in each irreducible representation of the octahedral group. We compare our calculations of nucleon excited states with the low-lying experimental spectrum. There is reasonable agreement for the pattern of states.

  13. Self-consistent velocity dispersions and mass spectra in the protoplanetary cloud

    NASA Astrophysics Data System (ADS)

    Barge, P.; Pellat, R.

    1990-06-01

    The Hornung et al. (1985) kinetic formalism characterizes the velocity dispersions of the planetesimals governing the accumulation of the planets; the equilibrium that arises in the competition between encounters and impacts is describable by steady-state equations for the velocity dispersions. On these bases, in conjunction with an assumed mass-spectrum power-law, it can be concluded that velocity dispersion is driven by the most massive objects and is nearly the same for each population, in cases where large bodies dominate, while in small body-dominated cases, an equipartition of kinetic energy arises from dynamical friction.

  14. Mass spectra stimulated by O+ and Ar+ interacting with a surface.

    NASA Technical Reports Server (NTRS)

    Siegel, M. W.; Krauss, R. H.; Boring, J. W.

    1972-01-01

    Beams of O(+) and Ar(+) in the energy range from 100 to 300 eV were directed into an aperture in one face of a copper box. The mass spectrum from a similar aperture in an adjacent face was observed with the aid of a commercial RF quadrupole spectrometer. On the basis of the results obtained it is reported that O(+) beams at about 200 eV may be essentially lost after a few collisions with a surface, in agreement with similar conclusions about atomic oxygen at thermal energies.

  15. CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra

    NASA Astrophysics Data System (ADS)

    Novák, Jiří; Lemr, Karel; Schug, Kevin A.; Havlíček, Vladimír

    2015-07-01

    Nonribosomal peptides have a wide range of biological and medical applications. Their identification by tandem mass spectrometry remains a challenging task. A new open-source de novo peptide identification engine CycloBranch was developed and successfully applied in identification or detailed characterization of 11 linear, cyclic, branched, and branch-cyclic peptides. CycloBranch is based on annotated building block databases the size of which is defined by the user according to ribosomal or nonribosomal peptide origin. The current number of involved nonisobaric and isobaric building blocks is 287 and 521, respectively. Contrary to all other peptide sequencing tools utilizing either peptide libraries or peptide fragment libraries, CycloBranch represents a true de novo sequencing engine developed for accurate mass spectrometric data. It is a stand-alone and cross-platform application with a graphical and user-friendly interface; it supports mzML, mzXML, mgf, txt, and baf file formats and can be run in parallel on multiple threads. It can be downloaded for free from http://ms.biomed.cas.cz/cyclobranch/, where the User's manual and video tutorials can be found.

  16. Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra.

    PubMed

    Halloran, John T; Bilmes, Jeff A; Noble, William S

    2016-08-01

    A central problem in mass spectrometry analysis involves identifying, for each observed tandem mass spectrum, the corresponding generating peptide. We present a dynamic Bayesian network (DBN) toolkit that addresses this problem by using a machine learning approach. At the heart of this toolkit is a DBN for Rapid Identification (DRIP), which can be trained from collections of high-confidence peptide-spectrum matches (PSMs). DRIP's score function considers fragment ion matches using Gaussians rather than fixed fragment-ion tolerances and also finds the optimal alignment between the theoretical and observed spectrum by considering all possible alignments, up to a threshold that is controlled using a beam-pruning algorithm. This function not only yields state-of-the art database search accuracy but also can be used to generate features that significantly boost the performance of the Percolator postprocessor. The DRIP software is built upon a general purpose DBN toolkit (GMTK), thereby allowing a wide variety of options for user-specific inference tasks as well as facilitating easy modifications to the DRIP model in future work. DRIP is implemented in Python and C++ and is available under Apache license at http://melodi-lab.github.io/dripToolkit .

  17. Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra.

    PubMed

    Halloran, John T; Bilmes, Jeff A; Noble, William S

    2016-08-01

    A central problem in mass spectrometry analysis involves identifying, for each observed tandem mass spectrum, the corresponding generating peptide. We present a dynamic Bayesian network (DBN) toolkit that addresses this problem by using a machine learning approach. At the heart of this toolkit is a DBN for Rapid Identification (DRIP), which can be trained from collections of high-confidence peptide-spectrum matches (PSMs). DRIP's score function considers fragment ion matches using Gaussians rather than fixed fragment-ion tolerances and also finds the optimal alignment between the theoretical and observed spectrum by considering all possible alignments, up to a threshold that is controlled using a beam-pruning algorithm. This function not only yields state-of-the art database search accuracy but also can be used to generate features that significantly boost the performance of the Percolator postprocessor. The DRIP software is built upon a general purpose DBN toolkit (GMTK), thereby allowing a wide variety of options for user-specific inference tasks as well as facilitating easy modifications to the DRIP model in future work. DRIP is implemented in Python and C++ and is available under Apache license at http://melodi-lab.github.io/dripToolkit . PMID:27397138

  18. Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST.

    PubMed

    López-Ferrer, Daniel; Martínez-Bartolomé, Salvador; Villar, Margarita; Campillos, Mónica; Martín-Maroto, Fernando; Vázquez, Jesús

    2004-12-01

    Recent technological advances have made multidimensional peptide separation techniques coupled with tandem mass spectrometry the method of choice for high-throughput identification of proteins. Due to these advances, the development of software tools for large-scale, fully automated, unambiguous peptide identification is highly necessary. In this work, we have used as a model the nuclear proteome from Jurkat cells and present a processing algorithm that allows accurate predictions of random matching distributions, based on the two SEQUEST scores Xcorr and DeltaCn. Our method permits a very simple and precise calculation of the probabilities associated with individual peptide assignments, as well as of the false discovery rate among the peptides identified in any experiment. A further mathematical analysis demonstrates that the score distributions are highly dependent on database size and precursor mass window and suggests that the probability associated with SEQUEST scores depends on the number of candidate peptide sequences available for the search. Our results highlight the importance of adjusting the filtering criteria to discriminate between correct and incorrect peptide sequences according to the circumstances of each particular experiment.

  19. Photon spectra and radiative properties of supercritical accretion flows with Comptonizing outflows around stellar-mass black holes

    NASA Astrophysics Data System (ADS)

    Kawashima, Tomohisa; Ohsuga, Ken; Mineshige, Shin; Heinzeller, Dominikus; Matsumoto, Ryoji

    Ultraluminous X-ray sources (ULXs) have recently been found in the off-center region of nearby external galaxies. The typical photon luminosities of ULXs range 1039.5-41 [erg/s], which ex-ceeds the Eddington luminosity for neutron stars and stellar-mass black holes. There are two possible models considered to account for such large photon luminosities: subcritical accretion (i.e., accretion below the Eddington accretion rate) onto an intermediate-mass black hole and supercritical accretion (i.e., accretion exceeding the Eddington accretion rate) onto a stellar-mass black hole. Since the black hole masses of ULXs are poorly known at present, we cannot discriminate between these two models. The study of radiation spectra of supercritical accre-tion flows may give a clue to resolve this issue. We calculated X-ray spectra of supercritical accretion flows with mildly hot outflows by Monte-Carlo techniques using two-dimensional ra-diation hydrodynamic simulation data of Kawashima et al. (2009). Our method is based on Pozdnyakov et al. (1977), and we incorporated radiative processes such as the modified black-body radiation with special relativistic effects (i.e., the Doppler shift and the aberration) at the photosphere, the free-free absorption, the photon trapping effect, the thermal Comptoniza-tion, and the bulk Comptonization. We found that the thermal inverse Compton scattering by electrons of the outflow affects the spectral energy distribution (SED) of the supercritical accretion flow. The fraction of the hard emission increases as the mass accretion rate increases (i.e., the photon luminosity increases). When the isotropic X-ray luminosity is below about 10 Eddington luminosity, the SED is similar to that of the slim disk state (i.e., the one-dimensional model of the supercritical accretion flow). By contrast, when the isotropic X-ray luminosity is larger than about 10 Eddington luminosity, the SED becomes harder at high energy region and deviates from the slim

  20. Simultaneous factor analysis of organic particle and gas mass spectra: AMS and PTR-MS measurements at an urban site

    NASA Astrophysics Data System (ADS)

    Slowik, J. G.; Vlasenko, A.; McGuire, M.; Evans, G. J.; Abbatt, J. P. D.

    2009-03-01

    During the winter component of the SPORT (Seasonal Particle Observations in the Region of Toronto) field campaign, particulate non-refractory chemical composition and concentration of selected volatile organic compounds (VOCs) were measured by an Aerodyne time-of-flight aerosol mass spectrometer (AMS) and a proton transfer reaction-mass spectrometer (PTR-MS), respectively. Sampling was performed in downtown Toronto ~15 m from a major road. The mass spectra from the AMS and PTR-MS were combined into a unified dataset, which was analyzed using positive matrix factorization (PMF). The two instruments were given equal weight in the PMF analysis by application of a scaling factor to the uncertainties of each instrument. A residual based metric, Δesc, was used to evaluate the relative weight. The PMF analysis yielded a 5-factor solution that included factors characteristic of regional transport, local traffic emissions, charbroiling, and oxidative processing. The unified dataset provides information on particle and VOC sources and atmospheric processing that cannot be obtained from the datasets of the individual instruments, such as apportionment of oxygenated VOCs to direct emission sources vs. secondary reaction products, improved correlation of oxygenated aerosol factors with photochemical age, and increased detail regarding the composition of oxygenated organic aerosol factors. This analysis represents the first application of PMF to a unified AMS/PTR-MS dataset.

  1. Simultaneous factor analysis of organic particle and gas mass spectra: AMS and PTR-MS measurements at an urban site

    NASA Astrophysics Data System (ADS)

    Slowik, J. G.; Vlasenko, A.; McGuire, M.; Evans, G. J.; Abbatt, J. P. D.

    2010-02-01

    During the winter component of the SPORT (Seasonal Particle Observations in the Region of Toronto) field campaign, particulate non-refractory chemical composition and concentration of selected volatile organic compounds (VOCs) were measured by an Aerodyne time-of-flight aerosol mass spectrometer (AMS) and a proton transfer reaction-mass spectrometer (PTR-MS), respectively. Sampling was performed in downtown Toronto ~15 m from a major road. The mass spectra from the AMS and PTR-MS were combined into a unified dataset, which was analysed using positive matrix factorization (PMF). The two instruments were given balanced weight in the PMF analysis by the application of a scaling factor to the uncertainties of each instrument. A residual based metric, Δesc, was used to evaluate the instrument relative weight within each solution. The PMF analysis yielded a 6-factor solution that included factors characteristic of regional transport, local traffic emissions, charbroiling and oxidative processing. The unified dataset provides information on emission sources (particle and VOC) and atmospheric processing that cannot be obtained from the datasets of the individual instruments: (1) apportionment of oxygenated VOCs to either direct emission sources or secondary reaction products; (2) improved correlation of oxygenated aerosol factors with photochemical age; and (3) increased detail regarding the composition of oxygenated organic aerosol factors. This analysis represents the first application of PMF to a unified AMS/PTR-MS dataset.

  2. An application of artificial intelligence to the interpretation of mass spectra.

    NASA Technical Reports Server (NTRS)

    Buchanan, B. G.; Duffield, A. M.; Robertson, A. V.

    1971-01-01

    Description of the DENDRAL (Dendritic Algorithm) project, the objectives of which were to base the computer program on an alogorithm that generates an exhaustive, nonredundant list of all the structural isomers of a given chemical composition, and to devise a computer program that would perform an organic structure determination, given a molecular formula and a mass spectrum. This program is called 'Heuristic DENDRAL' and it operates by using the known structure/spectrum correlations to constrain the DENDRAL isomer generator to produce a single isomer for that composition. The collaboration of chemists and computer scientists has produced a tool of some practical utility from the chemical viewpoint, and an interesting program from the viewpoint of artificial intelligence.

  3. Rest-frame Optical Spectra and Black Hole Masses of 3

    NASA Astrophysics Data System (ADS)

    Jun, Hyunsung David; Im, Myungshin; Lee, Hyung Mok; Ohyama, Youichi; Woo, Jong-Hak; Fan, Xiaohui; Goto, Tomotsugu; Kim, Dohyeong; Kim, Ji Hoon; Kim, Minjin; Lee, Myung Gyoon; Nakagawa, Takao; Pearson, Chris; Serjeant, Stephen

    2015-06-01

    We present the rest-frame optical spectral properties of 155 luminous quasars at 3.3 < z < 6.4 taken with the AKARI space telescope, including the first detection of the Hα emission line as far out as z ˜ 6. We extend the scaling relation between the rest-frame optical continuum and the line luminosity of active galactic nuclei (AGNs) to the high-luminosity, high-redshift regime that has rarely been probed before. Remarkably, we find that a single log-linear relation can be applied to the 5100 Å and Hα AGN luminosities over a wide range of luminosity (1042 < {{L}5100} < 1047 ergs s-1) or redshift (0 < z < 6), suggesting that the physical mechanism governing this relation is unchanged from z = 0 to 6, over five decades in luminosity. Similar scaling relations are found between the optical and the UV continuum luminosities or line widths. Applying the scaling relations to the Hβ black hole (BH) mass ({{M}BH}) estimator of local AGNs, we derive the {{M}BH} estimators based on the Hα, Mg ii, and C iv lines, finding that the UV-line-based masses are overall consistent with the Balmer-line-based, but with a large intrinsic scatter of 0.40 dex for the C iv estimates. Our 43 {{M}BH} estimates from Hα confirm the existence of BHs as massive as ˜ {{10}10} {{M}⊙ } out to z ˜ 5 and provide a secure footing for previous results from Mg ii-line-based studies that a rapid {{M}BH} growth has occurred in the early universe.

  4. STELLAR MASS-TO-LIGHT RATIOS FROM GALAXY SPECTRA: HOW ACCURATE CAN THEY BE?

    SciTech Connect

    Gallazzi, Anna; Bell, Eric F. E-mail: ericbell@umich.edu

    2009-12-01

    Stellar masses play a crucial role in the exploration of galaxy properties and the evolution of the galaxy population. In this paper, we explore the minimum possible uncertainties in stellar mass-to-light ratios (M {sub *}/L) from the assumed star formation history (SFH) and metallicity distribution, with the goals of providing a minimum set of requirements for observational studies. We use a large Monte Carlo library of SFHs to study as a function of galaxy spectral type and signal-to-noise ratio (S/N) the statistical uncertainties of M {sub *}/L values using either absorption-line data or broadband colors. The accuracy of M {sub *}/L estimates can be significantly improved by using metal-sensitive indices in combination with age-sensitive indices, in particular for galaxies with intermediate-age or young stellar populations. While M {sub *}/L accuracy clearly depends on the spectral S/N, there is no significant gain in improving the S/N much above 50 pixel{sup -1} and limiting uncertainties of {approx}0.03 dex are reached. Assuming that dust is accurately corrected or absent and that the redshift is known, color-based M {sub *}/L estimates are only slightly more uncertain than spectroscopic estimates (at comparable spectroscopic and photometric quality), but are more easily affected by systematic biases. This is the case in particular for galaxies with bursty SFHs (high H{delta} {sub A} at fixed D4000 {sub n}), the M {sub *}/L of which cannot be constrained any better than {approx}0.15 dex with any indicators explored here. Finally, we explore the effects of the assumed prior distribution in SFHs and metallicity, finding them to be higher for color-based estimates.

  5. Improved Cell Typing by Charge-State Deconvolution of matrix-assisted laser desorption/ionization Mass Spectra

    SciTech Connect

    Wilkes, Jon G.; Buzantu, Dan A.; Dare, Diane J.; Dragan, Yvonne P.; Chiarelli, M. Paul; Holland, Ricky D.; Beaudoin, Michael; Heinze, Thomas M.; Nayak, Rajesh; Shvartsburg, Alexandre A.

    2006-05-30

    Robust, specific, and rapid identification of toxic strains of bacteria and viruses, to guide the mitigation of their adverse health effects and optimum implementation of other response actions, remains a major analytical challenge. This need has driven the development of methods for classification of microorganisms using mass spectrometry, particularly matrix-assisted laser desorption ionization MS (MALDI) that allows high throughput analyses with minimum sample preparation. We describe a novel approach to cell typing based on pattern recognition of MALDI spectra, which involves charge-state deconvolution in conjunction with a new correlation analysis procedure. The method is applicable to both prokaryotic and eukaryotic cells. Charge-state deconvolution improves the quantitative reproducibility of spectra because multiply-charged ions resulting from the same biomarker attaching a different number of protons are recognized and their abundances are combined. This allows a clearer distinction of bacterial strains or of cancerous and normal liver cells. Improved class distinction provided by charge-state deconvolution was demonstrated by cluster spacing on canonical variate score charts and by correlation analyses. Deconvolution may enhance detection of early disease state or therapy progress markers in various tissues analyzed by MALDI.

  6. Size Effect on Nuclear Gamma-Ray Energy Spectra Acquired by Different Sized CeBr3, LaBr3:Ce, and NaI:Tl Gamma-Ray Detectors

    SciTech Connect

    Guss, Paul; Reed, Michael; Yuan, Ding; Beller, Denis; Cutler, Matthew; Contreras, Chris; Mukhopadhyay, Sanjoy; Wilde, Scott UNLV

    2014-03-01

    Gamma-ray energy spectra were acquired for different sizes of cerium tribromide (CeBr3), cerium-doped lanthanum tribromide (LaBr3:Ce), and thallium-doped sodium iodide (NaI:Tl) detectors. A comparison was conducted of the energy resolution and detection efficiency of these scintillator detectors for different sizes of detectors. The results of this study are consistent with the observation that for each size detector, LaBr3:Ce offers better resolution than either a CeBr3 or NaI:Tl detector of the same size. In addition, CeBr3 and LaBr3:Ce detectors could resolve some closely spaced peaks in the spectra of several radioisotopes that NaI:Tl could not. As the detector size increased, all three detector materials exhibited higher efficiency, albeit with slightly reduced resolution. Significantly, the very low intrinsic activity of CeBr3 is also demonstrated in this study, which, when combined with energy resolution characteristics for a range of detector sizes, could lead to an improved ability to detect special nuclear materials compared to the other detectors.

  7. The mass spectra, hierarchy and cosmology of B-L MSSM heterotic compactifications

    SciTech Connect

    Ambroso, Michael; Ovrut, Burt A.

    2011-04-10

    The matter spectrum of the MSSM, including three right-handed neutrino supermultiplets and one pair of Higgs-Higgs conjugate superfields, can be obtained by compactifying the E₈ x E₈ heterotic string and M-theory on Calabi-Yau manifolds with specific SU(4) vector bundles. These theories have the standard model gauge group augmented by an additional gauged U(1)B-L. Their minimal content requires that the B-L gauge symmetry be spontaneously broken by a vacuum expectation value of at least one right-handed neutrino. In previous papers, we presented the results of a quasi-analytic renormalization group analysis showing that B-L gauge symmetry is indeed radiatively broken with an appropriate B-L/electroweak hierarchy. In this paper, we extend these results by 1) enlarging the initial parameter space and 2) explicitly calculating all renormalization group equations numerically. The regions of the initial parameter space leading to realistic vacua are presented and the B-L/electroweak hierarchy computed over these regimes. At representative points, the mass spectrum for all particles and Higgs fields is calculated and shown to be consistent with present experimental bounds. Some fundamental phenomenological signatures of a non-zero right-handed neutrino expectation value are discussed, particularly the cosmology and proton lifetime arising from induced lepton and baryon number violating interactions.

  8. The mass spectra, hierarchy and cosmology of B-L MSSM heterotic compactifications

    DOE PAGES

    Ambroso, Michael; Ovrut, Burt A.

    2011-04-10

    The matter spectrum of the MSSM, including three right-handed neutrino supermultiplets and one pair of Higgs-Higgs conjugate superfields, can be obtained by compactifying the E₈ x E₈ heterotic string and M-theory on Calabi-Yau manifolds with specific SU(4) vector bundles. These theories have the standard model gauge group augmented by an additional gauged U(1)B-L. Their minimal content requires that the B-L gauge symmetry be spontaneously broken by a vacuum expectation value of at least one right-handed neutrino. In previous papers, we presented the results of a quasi-analytic renormalization group analysis showing that B-L gauge symmetry is indeed radiatively broken with anmore » appropriate B-L/electroweak hierarchy. In this paper, we extend these results by 1) enlarging the initial parameter space and 2) explicitly calculating all renormalization group equations numerically. The regions of the initial parameter space leading to realistic vacua are presented and the B-L/electroweak hierarchy computed over these regimes. At representative points, the mass spectrum for all particles and Higgs fields is calculated and shown to be consistent with present experimental bounds. Some fundamental phenomenological signatures of a non-zero right-handed neutrino expectation value are discussed, particularly the cosmology and proton lifetime arising from induced lepton and baryon number violating interactions.« less

  9. A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls

    PubMed Central

    Titulaer, Mark K; Siccama, Ivar; Dekker, Lennard J; van Rijswijk, Angelique LCT; Heeren, Ron MA; Sillevis Smitt, Peter A; Luider, Theo M

    2006-01-01

    Background Statistical comparison of peptide profiles in biomarker discovery requires fast, user-friendly software for high throughput data analysis. Important features are flexibility in changing input variables and statistical analysis of peptides that are differentially expressed between patient and control groups. In addition, integration the mass spectrometry data with the results of other experiments, such as microarray analysis, and information from other databases requires a central storage of the profile matrix, where protein id's can be added to peptide masses of interest. Results A new database application is presented, to detect and identify significantly differentially expressed peptides in peptide profiles obtained from body fluids of patient and control groups. The presented modular software is capable of central storage of mass spectra and results in fast analysis. The software architecture consists of 4 pillars, 1) a Graphical User Interface written in Java, 2) a MySQL database, which contains all metadata, such as experiment numbers and sample codes, 3) a FTP (File Transport Protocol) server to store all raw mass spectrometry files and processed data, and 4) the software package R, which is used for modular statistical calculations, such as the Wilcoxon-Mann-Whitney rank sum test. Statistic analysis by the Wilcoxon-Mann-Whitney test in R demonstrates that peptide-profiles of two patient groups 1) breast cancer patients with leptomeningeal metastases and 2) prostate cancer patients in end stage disease can be distinguished from those of control groups. Conclusion The database application is capable to distinguish patient Matrix Assisted Laser Desorption Ionization (MALDI-TOF) peptide profiles from control groups using large size datasets. The modular architecture of the application makes it possible to adapt the application to handle also large sized data from MS/MS- and Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry

  10. A versatile detector system to measure the change states, mass compositions and energy spectra of interplanetary and magnetosphere ions

    NASA Technical Reports Server (NTRS)

    Gloeckler, G.

    1977-01-01

    An instrument is described for measuring the mass and charge state composition as well as the energy spectra and angular distributions of 0.5 to 350 kev/charge ions in interplanetary space and in magnetospheres of planets such as Jupiter and earth. Electrostatic deflection combined with a time-of-flight and energy measurement allows three-parameter analysis of output signals from which the mass, charge states, and energy are determined. Post-acceleration by 30 kV extends the energy range of the detector system into the solar wind and magnetosphere plasma regime. Isotopes of H and He are easily resolved as are individual elements up to Ne and the dominant elements up to and including Fe. This instrument has an extremely large dynamic range in intensity and is sensitive to rare elements even in the presence of high intensity radiation, and is adapted for interplanetary, deep-space, and out-of-the-ecliptic missions, as well as for flights on spacecraft orbiting Jupiter and earth.

  11. Dielectron mass spectra from Au+Au collisions at √[s(NN)]=200  GeV.

    PubMed

    Adamczyk, L; Adkins, J K; Agakishiev, G; Aggarwal, M M; Ahammed, Z; Alekseev, I; Alford, J; Anson, C D; Aparin, A; Arkhipkin, D; Aschenauer, E C; Averichev, G S; Banerjee, A; Barnovska, Z; Beavis, D R; Bellwied, R; Bhasin, A; Bhati, A K; Bhattarai, P; Bichsel, H; Bielcik, J; Bielcikova, J; Bland, L C; Bordyuzhin, I G; Borowski, W; Bouchet, J; Brandin, A V; Brovko, S G; Bültmann, S; Bunzarov, I; Burton, T P; Butterworth, J; Caines, H; Calderón de la Barca Sánchez, M; Cebra, D; Cendejas, R; Cervantes, M C; Chaloupka, P; Chang, Z; Chattopadhyay, S; Chen, H F; Chen, J H; Chen, L; Cheng, J; Cherney, M; Chikanian, A; Christie, W; Chwastowski, J; Codrington, M J M; Cramer, J G; Crawford, H J; Cui, X; Das, S; Davila Leyva, A; De Silva, L C; Debbe, R R; Dedovich, T G; Deng, J; Derevschikov, A A; Derradi de Souza, R; Dhamija, S; di Ruzza, B; Didenko, L; Dilks, C; Ding, F; Djawotho, P; Dong, X; Drachenberg, J L; Draper, J E; Du, C M; Dunkelberger, L E; Dunlop, J C; Efimov, L G; Engelage, J; Engle, K S; Eppley, G; Eun, L; Evdokimov, O; Fatemi, R; Fazio, S; Fedorisin, J; Filip, P; Finch, E; Fisyak, Y; Flores, C E; Gagliardi, C A; Gangadharan, D R; Garand, D; Geurts, F; Gibson, A; Girard, M; Gliske, S; Grosnick, D; Guo, Y; Gupta, A; Gupta, S; Guryn, W; Haag, B; Hajkova, O; Hamed, A; Han, L-X; Haque, R; Harris, J W; Heppelmann, S; Hirsch, A; Hoffmann, G W; Hofman, D J; Horvat, S; Huang, B; Huang, H Z; Huang, X; Huck, P; Humanic, T J; Igo, G; Jacobs, W W; Jang, H; Judd, E G; Kabana, S; Kalinkin, D; Kang, K; Kauder, K; Ke, H W; Keane, D; Kechechyan, A; Kesich, A; Khan, Z H; Kikola, D P; Kisel, I; Kisiel, A; Koetke, D D; Kollegger, T; Konzer, J; Koralt, I; Korsch, W; Kotchenda, L; Kravtsov, P; Krueger, K; Kulakov, I; Kumar, L; Kycia, R A; Lamont, M A C; Landgraf, J M; Landry, K D; Lauret, J; Lebedev, A; Lednicky, R; Lee, J H; LeVine, M J; Li, C; Li, W; Li, X; Li, X; Li, Y; Li, Z M; Lima, L M; Lisa, M A; Liu, F; Ljubicic, T; Llope, W J; Longacre, R S; Luo, X; Ma, G L; Ma, Y G; Madagodagettige Don, D M M D; Mahapatra, D P; Majka, R; Margetis, S; Markert, C; Masui, H; Matis, H S; McDonald, D; McShane, T S; Minaev, N G; Mioduszewski, S; Mohanty, B; Mondal, M M; Morozov, D A; Munhoz, M G; Mustafa, M K; Nandi, B K; Nasim, Md; Nayak, T K; Nelson, J M; Nogach, L V; Noh, S Y; Novak, J; Nurushev, S B; Odyniec, G; Ogawa, A; Oh, K; Ohlson, A; Okorokov, V; Oldag, E W; Oliveira, R A N; Pachr, M; Page, B S; Pal, S K; Pan, Y X; Pandit, Y; Panebratsev, Y; Pawlak, T; Pawlik, B; Pei, H; Perkins, C; Peryt, W; Pile, P; Planinic, M; Pluta, J; Plyku, D; Poljak, N; Porter, J; Poskanzer, A M; Pruthi, N K; Przybycien, M; Pujahari, P R; Qiu, H; Quintero, A; Ramachandran, S; Raniwala, R; Raniwala, S; Ray, R L; Riley, C K; Ritter, H G; Roberts, J B; Rogachevskiy, O V; Romero, J L; Ross, J F; Roy, A; Ruan, L; Rusnak, J; Sahoo, N R; Sahu, P K; Sakrejda, I; Salur, S; Sandacz, A; Sandweiss, J; Sangaline, E; Sarkar, A; Schambach, J; Scharenberg, R P; Schmah, A M; Schmidke, W B; Schmitz, N; Seger, J; Seyboth, P; Shah, N; Shahaliev, E; Shanmuganathan, P V; Shao, M; Sharma, B; Shen, W Q; Shi, S S; Shou, Q Y; Sichtermann, E P; Singaraju, R N; Skoby, M J; Smirnov, D; Smirnov, N; Solanki, D; Sorensen, P; deSouza, U G; Spinka, H M; Srivastava, B; Stanislaus, T D S; Stevens, J R; Stock, R; Strikhanov, M; Stringfellow, B; Suaide, A A P; Sumbera, M; Sun, X; Sun, X M; Sun, Y; Sun, Z; Surrow, B; Svirida, D N; Symons, T J M; Szanto de Toledo, A; Takahashi, J; Tang, A H; Tang, Z; Tarnowsky, T; Thomas, J H; Timmins, A R; Tlusty, D; Tokarev, M; Trentalange, S; Tribble, R E; Tribedy, P; Trzeciak, B A; Tsai, O D; Turnau, J; Ullrich, T; Underwood, D G; Van Buren, G; van Nieuwenhuizen, G; Vanfossen, J A; Varma, R; Vasconcelos, G M S; Vasiliev, A N; Vertesi, R; Videbæk, F; Viyogi, Y P; Vokal, S; Vossen, A; Wada, M; Wang, F; Wang, G; Wang, H; Wang, J S; Wang, X L; Wang, Y; Wang, Y; Webb, G; Webb, J C; Westfall, G D; Wieman, H; Wissink, S W; Witt, R; Wu, Y F; Xiao, Z; Xie, W; Xin, K; Xu, H; Xu, N; Xu, Q H; Xu, Y; Xu, Z; Yan, W; Yang, C; Yang, Y; Yang, Y; Ye, Z; Yepes, P; Yi, L; Yip, K; Yoo, I-K; Zawisza, Y; Zbroszczyk, H; Zha, W; Zhang, J B; Zhang, J L; Zhang, S; Zhang, X P; Zhang, Y; Zhang, Z P; Zhao, F; Zhao, J; Zhong, C; Zhu, X; Zhu, Y H; Zoulkarneeva, Y; Zyzak, M

    2014-07-11

    We report the STAR measurements of dielectron (e(+)e(-)) production at midrapidity (|y(ee)|<1) in Au+Au collisions at √[s(NN)]=200  GeV. The measurements are evaluated in different invariant mass regions with a focus on 0.30-0.76 (ρ-like), 0.76-0.80 (ω-like), and 0.98-1.05 (ϕ-like)   GeV/c(2). The spectrum in the ω-like and ϕ-like regions can be well described by the hadronic cocktail simulation. In the ρ-like region, however, the vacuum ρ spectral function cannot describe the shape of the dielectron excess. In this range, an enhancement of 1.77±0.11(stat)±0.24(syst)±0.33(cocktail) is determined with respect to the hadronic cocktail simulation that excludes the ρ meson. The excess yield in the ρ-like region increases with the number of collision participants faster than the ω and ϕ yields. Theoretical models with broadened ρ contributions through interactions with constituents in the hot QCD medium provide a consistent description of the dilepton mass spectra for the measurement presented here and the earlier data at the Super Proton Synchrotron energies. PMID:25062167

  12. Dielectron mass spectra from Au+Au collisions at √[s(NN)]=200  GeV.

    PubMed

    Adamczyk, L; Adkins, J K; Agakishiev, G; Aggarwal, M M; Ahammed, Z; Alekseev, I; Alford, J; Anson, C D; Aparin, A; Arkhipkin, D; Aschenauer, E C; Averichev, G S; Banerjee, A; Barnovska, Z; Beavis, D R; Bellwied, R; Bhasin, A; Bhati, A K; Bhattarai, P; Bichsel, H; Bielcik, J; Bielcikova, J; Bland, L C; Bordyuzhin, I G; Borowski, W; Bouchet, J; Brandin, A V; Brovko, S G; Bültmann, S; Bunzarov, I; Burton, T P; Butterworth, J; Caines, H; Calderón de la Barca Sánchez, M; Cebra, D; Cendejas, R; Cervantes, M C; Chaloupka, P; Chang, Z; Chattopadhyay, S; Chen, H F; Chen, J H; Chen, L; Cheng, J; Cherney, M; Chikanian, A; Christie, W; Chwastowski, J; Codrington, M J M; Cramer, J G; Crawford, H J; Cui, X; Das, S; Davila Leyva, A; De Silva, L C; Debbe, R R; Dedovich, T G; Deng, J; Derevschikov, A A; Derradi de Souza, R; Dhamija, S; di Ruzza, B; Didenko, L; Dilks, C; Ding, F; Djawotho, P; Dong, X; Drachenberg, J L; Draper, J E; Du, C M; Dunkelberger, L E; Dunlop, J C; Efimov, L G; Engelage, J; Engle, K S; Eppley, G; Eun, L; Evdokimov, O; Fatemi, R; Fazio, S; Fedorisin, J; Filip, P; Finch, E; Fisyak, Y; Flores, C E; Gagliardi, C A; Gangadharan, D R; Garand, D; Geurts, F; Gibson, A; Girard, M; Gliske, S; Grosnick, D; Guo, Y; Gupta, A; Gupta, S; Guryn, W; Haag, B; Hajkova, O; Hamed, A; Han, L-X; Haque, R; Harris, J W; Heppelmann, S; Hirsch, A; Hoffmann, G W; Hofman, D J; Horvat, S; Huang, B; Huang, H Z; Huang, X; Huck, P; Humanic, T J; Igo, G; Jacobs, W W; Jang, H; Judd, E G; Kabana, S; Kalinkin, D; Kang, K; Kauder, K; Ke, H W; Keane, D; Kechechyan, A; Kesich, A; Khan, Z H; Kikola, D P; Kisel, I; Kisiel, A; Koetke, D D; Kollegger, T; Konzer, J; Koralt, I; Korsch, W; Kotchenda, L; Kravtsov, P; Krueger, K; Kulakov, I; Kumar, L; Kycia, R A; Lamont, M A C; Landgraf, J M; Landry, K D; Lauret, J; Lebedev, A; Lednicky, R; Lee, J H; LeVine, M J; Li, C; Li, W; Li, X; Li, X; Li, Y; Li, Z M; Lima, L M; Lisa, M A; Liu, F; Ljubicic, T; Llope, W J; Longacre, R S; Luo, X; Ma, G L; Ma, Y G; Madagodagettige Don, D M M D; Mahapatra, D P; Majka, R; Margetis, S; Markert, C; Masui, H; Matis, H S; McDonald, D; McShane, T S; Minaev, N G; Mioduszewski, S; Mohanty, B; Mondal, M M; Morozov, D A; Munhoz, M G; Mustafa, M K; Nandi, B K; Nasim, Md; Nayak, T K; Nelson, J M; Nogach, L V; Noh, S Y; Novak, J; Nurushev, S B; Odyniec, G; Ogawa, A; Oh, K; Ohlson, A; Okorokov, V; Oldag, E W; Oliveira, R A N; Pachr, M; Page, B S; Pal, S K; Pan, Y X; Pandit, Y; Panebratsev, Y; Pawlak, T; Pawlik, B; Pei, H; Perkins, C; Peryt, W; Pile, P; Planinic, M; Pluta, J; Plyku, D; Poljak, N; Porter, J; Poskanzer, A M; Pruthi, N K; Przybycien, M; Pujahari, P R; Qiu, H; Quintero, A; Ramachandran, S; Raniwala, R; Raniwala, S; Ray, R L; Riley, C K; Ritter, H G; Roberts, J B; Rogachevskiy, O V; Romero, J L; Ross, J F; Roy, A; Ruan, L; Rusnak, J; Sahoo, N R; Sahu, P K; Sakrejda, I; Salur, S; Sandacz, A; Sandweiss, J; Sangaline, E; Sarkar, A; Schambach, J; Scharenberg, R P; Schmah, A M; Schmidke, W B; Schmitz, N; Seger, J; Seyboth, P; Shah, N; Shahaliev, E; Shanmuganathan, P V; Shao, M; Sharma, B; Shen, W Q; Shi, S S; Shou, Q Y; Sichtermann, E P; Singaraju, R N; Skoby, M J; Smirnov, D; Smirnov, N; Solanki, D; Sorensen, P; deSouza, U G; Spinka, H M; Srivastava, B; Stanislaus, T D S; Stevens, J R; Stock, R; Strikhanov, M; Stringfellow, B; Suaide, A A P; Sumbera, M; Sun, X; Sun, X M; Sun, Y; Sun, Z; Surrow, B; Svirida, D N; Symons, T J M; Szanto de Toledo, A; Takahashi, J; Tang, A H; Tang, Z; Tarnowsky, T; Thomas, J H; Timmins, A R; Tlusty, D; Tokarev, M; Trentalange, S; Tribble, R E; Tribedy, P; Trzeciak, B A; Tsai, O D; Turnau, J; Ullrich, T; Underwood, D G; Van Buren, G; van Nieuwenhuizen, G; Vanfossen, J A; Varma, R; Vasconcelos, G M S; Vasiliev, A N; Vertesi, R; Videbæk, F; Viyogi, Y P; Vokal, S; Vossen, A; Wada, M; Wang, F; Wang, G; Wang, H; Wang, J S; Wang, X L; Wang, Y; Wang, Y; Webb, G; Webb, J C; Westfall, G D; Wieman, H; Wissink, S W; Witt, R; Wu, Y F; Xiao, Z; Xie, W; Xin, K; Xu, H; Xu, N; Xu, Q H; Xu, Y; Xu, Z; Yan, W; Yang, C; Yang, Y; Yang, Y; Ye, Z; Yepes, P; Yi, L; Yip, K; Yoo, I-K; Zawisza, Y; Zbroszczyk, H; Zha, W; Zhang, J B; Zhang, J L; Zhang, S; Zhang, X P; Zhang, Y; Zhang, Z P; Zhao, F; Zhao, J; Zhong, C; Zhu, X; Zhu, Y H; Zoulkarneeva, Y; Zyzak, M

    2014-07-11

    We report the STAR measurements of dielectron (e(+)e(-)) production at midrapidity (|y(ee)|<1) in Au+Au collisions at √[s(NN)]=200  GeV. The measurements are evaluated in different invariant mass regions with a focus on 0.30-0.76 (ρ-like), 0.76-0.80 (ω-like), and 0.98-1.05 (ϕ-like)   GeV/c(2). The spectrum in the ω-like and ϕ-like regions can be well described by the hadronic cocktail simulation. In the ρ-like region, however, the vacuum ρ spectral function cannot describe the shape of the dielectron excess. In this range, an enhancement of 1.77±0.11(stat)±0.24(syst)±0.33(cocktail) is determined with respect to the hadronic cocktail simulation that excludes the ρ meson. The excess yield in the ρ-like region increases with the number of collision participants faster than the ω and ϕ yields. Theoretical models with broadened ρ contributions through interactions with constituents in the hot QCD medium provide a consistent description of the dilepton mass spectra for the measurement presented here and the earlier data at the Super Proton Synchrotron energies.

  13. Statistical analysis of fragmentation patterns of electron ionization mass spectra of enolized-trimethylsilylated anabolic androgenic steroids

    NASA Astrophysics Data System (ADS)

    Fragkaki, A. G.; Angelis, Y. S.; Tsantili-Kakoulidou, A.; Koupparis, M.; Georgakopoulos, C.

    2009-08-01

    Anabolic androgenic steroids (AAS) are included in the List of prohibited substances of the World Anti-Doping Agency (WADA) as substances abused to enhance athletic performance. Gas chromatography coupled to mass spectrometry (GC-MS) plays an important role in doping control analyses identifying AAS as their enolized-trimethylsilyl (TMS)-derivatives using the electron ionization (EI) mode. This paper explores the suitability of complementary GC-MS mass spectra and statistical analysis (principal component analysis, PCA and partial least squares-discriminant analysis, PLS-DA) to differentiate AAS as a function of their structural and conformational features expressed by their fragment ions. The results obtained showed that the application of PCA yielded a classification among the AAS molecules which became more apparent after applying PLS-DA to the dataset. The application of PLS-DA yielded a clear separation among the AAS molecules which were, thus, classified as: 1-ene-3-keto, 3-hydroxyl with saturated A-ring, 1-ene-3-hydroxyl, 4-ene-3-keto, 1,4-diene-3-keto and 3-keto with saturated A-ring anabolic steroids. The study of this paper also presents structurally diagnostic fragment ions and dissociation routes providing evidence for the presence of unknown AAS or chemically modified molecules known as designer steroids.

  14. Composite spectraPaper 10: the equal-mass binary HR 2030 (K0IIb+B8IV)

    NASA Astrophysics Data System (ADS)

    Griffin, R. E. M.; Griffin, R. F.

    2000-12-01

    We separate the spectra of the individual components of HR 2030, a sixth-magnitude composite-spectrum binary system, and show that they have types close to K0IIb and B8IV, and masses that are equal to within the precision of the measurements (mass ratio=1.00+/-0.03). The orbit appears to have a very small eccentricity, although reasons are given for believing that such eccentricity is spurious; it has a period of 66d and an inclination estimated at 30° to the line of sight. Our photometric model of the system confirms the luminosity types derived from the spectra and indicates an interstellar absorption of 0.4mag, in accord with the observed strength of the interstellar K line. We derive the physical parameters (Teff, Mbol, R, L) of the components, and calculate that the mass of each star is close to 4.0Msolar. We further show that the hot component (R=5.9+/-0.6Rsolar) has already evolved to a position significantly above the zero-age main sequence (ZAMS), and we propose that the primary (R=41+/-5Rsolar) is making its first ascent of the red-giant branch. From comparisons with evolutionary tracks, we deduce that the age of the binary (since its arrival at the ZAMS) is in the range 1-2×108yr. While we suspect that the components are sufficiently close for some tidal distortion to occur, the effects are not discernible in our data owing to the rather low orbital inclination. The system shows Sii in emission as a result of irradiation of the primary by the hot secondary, but in the optical spectrum we see little other clear evidence of interaction between the components even though the object has a relatively short period and is a strong X-ray source. On the other hand, Hipparcos photometry suggests the existence of a major non-uniformity of the surface of the primary star.

  15. A new method to discriminate secondary organic aerosols from different sources using high-resolution aerosol mass spectra

    NASA Astrophysics Data System (ADS)

    Heringa, M. F.; Decarlo, P. F.; Chirico, R.; Tritscher, T.; Clairotte, M.; Mohr, C.; Crippa, M.; Slowik, J. G.; Pfaffenberger, L.; Dommen, J.; Weingartner, E.; Prévôt, A. S. H.; Baltensperger, U.

    2011-10-01

    Organic aerosol (OA) represents a significant and often major fraction of the non-refractory PM1 (particulate matter with an aerodynamic diameter da < 1 μm) mass. Secondary organic aerosol (SOA) is an important contributor to the OA and can be formed from biogenic and anthropogenic precursors. Here we present results from the characterization of SOA produced from the emissions of three different anthropogenic sources. SOA from a log wood burner, a Euro 2 diesel car and a two-stroke Euro 2 scooter were characterized with an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-TOF-AMS) and compared to SOA from α-pinene. The emissions were sampled from the chimney/tailpipe by a heated inlet system and filtered before injection into a smog chamber. The gas phase emissions were irradiated by xenon arc lamps to initiate photo-chemistry which led to nucleation and subsequent particle growth by SOA production. Duplicate experiments were performed for each SOA type, with the averaged organic mass spectra in the m/z range 12-250 showing Pearson's r values >0.94 for the correlations between the different SOA types after 5 h of aging. High-resolution mass spectra (HR-MS) showed that the dominant peaks in the MS, m/z 43 and 44, are dominated by the oxygenated ions C2H3O+ and CO2+, respectively, similarly to the relatively fresh semi-volatile oxidized OA (SV-OOA) observed in the ambient aerosol. The atomic O : C ratios were found to be in the range of 0.25-0.55 with no major increase during the first 5 h of aging. On average, the diesel SOA showed the lowest O : C ratio followed by SOA from wood burning, α-pinene and the scooter emissions. Grouping the fragment ions based on their carbon number revealed that the SOA source with the highest O : C ratio had the largest fraction of small ions. Fragment ions containing up to 3 carbon atoms accounted for 66%, 68%, 72% and 76% of the organic spectrum of the SOA produced by the diesel car, wood burner, α-pinene and

  16. A new method to discriminate secondary organic aerosols from different sources using high-resolution aerosol mass spectra

    NASA Astrophysics Data System (ADS)

    Heringa, M. F.; Decarlo, P. F.; Chirico, R.; Tritscher, T.; Clairotte, M.; Mohr, C.; Crippa, M.; Slowik, J. G.; Pfaffenberger, L.; Dommen, J.; Weingartner, E.; Prévôt, A. S. H.; Baltensperger, U.

    2012-02-01

    Organic aerosol (OA) represents a significant and often major fraction of the non-refractory PM1 (particulate matter with an aerodynamic diameter da < 1 μm) mass. Secondary organic aerosol (SOA) is an important contributor to the OA and can be formed from biogenic and anthropogenic precursors. Here we present results from the characterization of SOA produced from the emissions of three different anthropogenic sources. SOA from a log wood burner, a Euro 2 diesel car and a two-stroke Euro 2 scooter were characterized with an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-TOF-AMS) and compared to SOA from α-pinene. The emissions were sampled from the chimney/tailpipe by a heated inlet system and filtered before injection into a smog chamber. The gas phase emissions were irradiated by xenon arc lamps to initiate photo-chemistry which led to nucleation and subsequent particle growth by SOA production. Duplicate experiments were performed for each SOA type, with the averaged organic mass spectra showing Pearson's r values >0.94 for the correlations between the four different SOA types after five hours of aging. High-resolution mass spectra (HR-MS) showed that the dominant peaks in the MS, m/z 43 and 44, are dominated by the oxygenated ions C2H3O+ and CO2+, respectively, similarly to the relatively fresh semi-volatile oxygenated OA (SV-OOA) observed in the ambient aerosol. The atomic O:C ratios were found to be in the range of 0.25-0.55 with no major increase during the first five hours of aging. On average, the diesel SOA showed the lowest O:C ratio followed by SOA from wood burning, α-pinene and the scooter emissions. Grouping the fragment ions revealed that the SOA source with the highest O:C ratio had the largest fraction of small ions. The HR data of the four sources could be clustered and separated using principal component analysis (PCA). The model showed a significant separation of the four SOA types and clustering of the duplicate

  17. Retrieval of Precise Radial Velocities from Near-infrared High-resolution Spectra of Low-mass Stars

    NASA Astrophysics Data System (ADS)

    Gao, Peter; Plavchan, P.; Gagné, J.; Furlan, E.; Bottom, M.; Anglada-Escudé, G.; White, R.; Davison, C. L.; Beichman, C.; Brinkworth, C.; Johnson, J.; Ciardi, D.; Wallace, K.; Mennesson, B.; von Braun, K.; Vasisht, G.; Prato, L.; Kane, S. R.; Tanner, A.; Crawford, T. J.; Latham, D.; Rougeot, R.; Geneser, C. S.; Catanzarite, J.

    2016-10-01

    Given that low-mass stars have intrinsically low luminosities at optical wavelengths and a propensity for stellar activity, it is advantageous for radial velocity (RV) surveys of these objects to use near-infrared (NIR) wavelengths. In this work, we describe and test a novel RV extraction pipeline dedicated to retrieving RVs from low-mass stars using NIR spectra taken by the CSHELL spectrograph at the NASA Infrared Telescope Facility, where a methane isotopologue gas cell is used for wavelength calibration. The pipeline minimizes the residuals between the observations and a spectral model composed of templates for the target star, the gas cell, and atmospheric telluric absorption; models of the line-spread function, continuum curvature, and sinusoidal fringing; and a parameterization of the wavelength solution. The stellar template is derived iteratively from the science observations themselves without a need for separate observations dedicated to retrieving it. Despite limitations from CSHELL’s narrow wavelength range and instrumental systematics, we are able to (1) obtain an RV precision of 35 m s-1 for the RV standard star GJ 15 A over a time baseline of 817 days, reaching the photon noise limit for our attained signal-to-noise ratio; (2) achieve ˜3 m s-1 RV precision for the M giant SV Peg over a baseline of several days and confirm its long-term RV trend due to stellar pulsations, as well as obtain nightly noise floors of ˜2-6 m s-1 and (3) show that our data are consistent with the known masses, periods, and orbital eccentricities of the two most massive planets orbiting GJ 876. Future applications of our pipeline to RV surveys using the next generation of NIR spectrographs, such as iSHELL, will enable the potential detection of super-Earths and mini-Neptunes in the habitable zones of M dwarfs.

  18. New characteristics of submicron aerosols and factor analysis of combined organic and inorganic aerosol mass spectra during winter in Beijing

    NASA Astrophysics Data System (ADS)

    Zhang, J. K.; Ji, D. S.; Liu, Z. R.; Hu, B.; Wang, L. L.; Huang, X. J.; Wang, Y. S.

    2015-07-01

    In recent years, an increasing amount of attention has been paid to heavy haze pollution in Beijing, China. In addition to Beijing's population of approximately 20 million and its 5 million vehicles, nearby cities and provinces are host to hundreds of heavily polluting industries. In this study, a comparison between observations in January 2013 and January 2014 showed that non-refractory PM1 (NR-PM1) pollution was weaker in January 2014, which was primarily caused by variations in meteorological conditions. For the first time, positive matrix factorization (PMF) was applied to the merged high-resolution mass spectra of organic and inorganic aerosols from aerosol mass spectrometer measurements in Beijing, and the sources and evolution of NR-PM1 in January 2014 were investigated. The two factors, NO3-OA1 and NO3-OA2, were primarily composed of ammonium nitrate, and each showed a different degree of oxidation and diurnal variation. The organic fraction of SO4-OA showed the highest degree of oxidation of all PMF factors. The hydrocarbon-like organic aerosol (OA) and cooking OA factors contained negligible amounts of inorganic species. The coal combustion OA factor contained a high contribution from chloride in its mass spectrum. The NR-PM1 composition showed significant variations in January 2014, in which the contribution of nitrate clearly increased during heavy pollution events. The most effective way to control fine particle pollution in Beijing is through joint prevention and control measures at the regional level, rather than a focus on an individual city, especially for severe haze events.

  19. Acquired lymphangiectasis.

    PubMed

    Celis, A V; Gaughf, C N; Sangueza, O P; Gourdin, F W

    1999-01-01

    Acquired lymphangiectasis is a dilatation of lymphatic vessels that can result as a complication of surgical intervention and radiation therapy for malignancy. Acquired lymphangiectasis shares clinical and histologic features with the congenital lesion, lymphangioma circumscriptum. Diagnosis and treatment of these vesiculo-bullous lesions is important because they may be associated with pain, chronic drainage, and cellulitis. We describe two patients who had these lesions after treatment for cancer and review the pertinent literature. Although a number of treatment options are available, we have found CO2 laser ablation particularly effective. PMID:9932832

  20. Rosetta/COSIMA: Laboratory time-of-flight secondary ion mass spectra of PAHs for in-situ detection in the cometary solid organic matter

    NASA Astrophysics Data System (ADS)

    Bardyn, A.; Briois, C.; Cottin, H.; Fray, N.; LeRoy, L.; Thirkell, L.; Hilchenbach, M.

    2014-07-01

    ESA's spacecraft called ROSETTA will reach the comet 67P/Churyumov- Gerasimenko in August 2014. During the escort phase of the mission, beginning after the lander (Philae) is released, the COmetary Secondary Ion Mass Analyzer (COSIMA) [1] carried on board will collect and analyse dust grains in the cometary coma. COSIMA is a time-of-flight secondary ion mass spectrometer (TOF-SIMS) with a high mass resolution m/Δ m of 1400 at mass m=100 amu (from FWHM) and mass range from 1 to 3500 amu. The investigations performed by COSIMA on solid cometary grains are aimed to analyze in situ their molecular, elemental, and isotopic composition. The spectra obtained with COSIMA, will be a combination of mass peaks of mineral and organic elements. The organics are expected to be minor peaks, making their identification not simple. To prepare for the future COSIMA spectra interpretation, the COSIMA team members have started to establish a library database of standardized mass spectra [2,3]. High statistics of positive and negative spectra of the samples were then taken in order to get molecular structure information. Polycyclic Aromatic Hydrocarbons (PAHs) are organic macromolecules that could survive harsh radiation environment. They are suspected to be responsible for unidentified infrared bands observed in diverse astrophysical environments. Many attempts were made to demonstrate the presence of PAHs in comets. Tentative attributions of fluorescence emission bands have been made of spectra taken during the Vega-2 mission [4,5], and recently on Stardust samples returned [6]. In this work, we have used the COSIMA prototype based in Orléans to analyze PAHs and alkanes molecules deposition on gold targets.

  1. Effects of Growth Medium on Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectra: a Case Study of Acetic Acid Bacteria

    PubMed Central

    Wieme, Anneleen D.; Spitaels, Freek; Aerts, Maarten; De Bruyne, Katrien; Van Landschoot, Anita

    2014-01-01

    The effect of the growth medium used on the matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectra generated and its consequences for species and strain level differentiation of acetic acid bacteria (AAB) were determined by using a set of 25 strains. The strains were grown on five different culture media that yielded a total of more than 600 mass spectra, including technical and biological replicates. The results demonstrate that the culture medium can have a profound effect on the mass spectra of AAB as observed in the presence and varying signal intensities of peak classes, in particular when culture media do not sustain optimal growth. The observed growth medium effects do not disturb species level differentiation but strongly affect the potential for strain level differentiation. The data prove that a well-constructed and robust MALDI-TOF mass spectrometry identification database should comprise mass spectra of multiple reference strains per species grown on different culture media to facilitate species and strain level differentiation. PMID:24362425

  2. reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

    PubMed

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W; Moritz, Robert L

    2015-11-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. Graphical Abstract ᅟ.

  3. reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

    PubMed

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W; Moritz, Robert L

    2015-11-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. Graphical Abstract ᅟ. PMID:26419769

  4. reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

    NASA Astrophysics Data System (ADS)

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

    2015-11-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website.

  5. reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

    PubMed Central

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

    2016-01-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contributes to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), that enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the following iterations. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. PMID:26419769

  6. Single Nanoparticle Mass Spectrometry as a High Temperature Kinetics Tool: Sublimation, Oxidation, and Emission Spectra of Hot Carbon Nanoparticles.

    PubMed

    Howder, Collin R; Long, Bryan A; Gerlich, Dieter; Alley, Rex N; Anderson, Scott L

    2015-12-17

    In single nanoparticle mass spectrometry, individual charged nanoparticles (NPs) are trapped in a quadrupole ion trap and detected optically, allowing their mass, charge, and optical properties to be monitored continuously. Previous experiments of this type probed NPs that were either fluorescent or large enough to detect by light scattering. Alternatively, small NPs can be heated to temperatures where thermally excited emission is strong enough to allow detection, and this approach should provide a new tool for measurements of sublimation and surface reaction kinetics of materials at high temperatures. As an initial test, we report a study of carbon NPs in the 20-50 nm range, heated by 10.6 μm, 532 nm, or 445 nm lasers. The kinetics for sublimation and oxidation of individual carbon NPs were studied, and a model is presented for the factors that control the NP temperature, including laser heating, and cooling by sublimation, buffer gas collisions, and radiation. The estimated NP temperatures were in the 1700-2000 K range, and the NP absorption cross sections ranged from ∼0.8 to 0.2% of the geometric cross sections for 532 nm and 10.6 μm excitation, respectively. Emission spectra of single NPs and small NP ensembles show a feature in the IR that appears to be the high energy tail of the thermal (blackbody-like) emission expected from hot particles but also a discrete feature peaking around 750 nm. Both the IR tail and 750 nm peak are observed for all particles and for both IR and visible laser excitation. No significant difference was observed between graphite and amorphous carbon NPs. PMID:26513667

  7. Rapid, Automated Determination of Elemental Compositions of Ions in Mass Spectra Obtained with an Open-Air Ion Source (2 of 2)

    EPA Science Inventory

    An inexpensive autosampler for a DART/TOFMS provides mass spectra from analytes absorbed on 76 cotton swab, wipe samples in 7.5 min. A field sample carrier simplifies sample collection and provides swabs nearly ready for analysis to the lab. Applications of the high throughput pr...

  8. Acquired hyperpigmentations*

    PubMed Central

    Cestari, Tania Ferreira; Dantas, Lia Pinheiro; Boza, Juliana Catucci

    2014-01-01

    Cutaneous hyperpigmentations are frequent complaints, motivating around 8.5% of all dermatological consultations in our country. They can be congenital, with different patterns of inheritance, or acquired in consequence of skin problems, systemic diseases or secondary to environmental factors. The vast majority of them are linked to alterations on the pigment melanin, induced by different mechanisms. This review will focus on the major acquired hyperpigmentations associated with increased melanin, reviewing their mechanisms of action and possible preventive measures. Particularly prominent aspects of diagnosis and therapy will be emphasized, with focus on melasma, post-inflammatory hyperpigmentation, periorbital pigmentation, dermatosis papulosa nigra, phytophotodermatoses, flagellate dermatosis, erythema dyschromicum perstans, cervical poikiloderma (Poikiloderma of Civatte), acanthosis nigricans, cutaneous amyloidosis and reticulated confluent dermatitis PMID:24626644

  9. c2d Spitzer IRS spectra of embedded low-mass young stars: gas-phase emission lines

    NASA Astrophysics Data System (ADS)

    Lahuis, F.; van Dishoeck, E. F.; Jørgensen, J. K.; Blake, G. A.; Evans, N. J.

    2010-09-01

    Context. A survey of mid-infrared gas-phase emission lines of H2, H2O and various atoms toward a sample of 43 embedded low-mass young stars in nearby star-forming regions is presented. The sources are selected from the Spitzer “Cores to Disks” (c2d) legacy program. Aims: The environment of embedded protostars is complex both in its physical structure (envelopes, outflows, jets, protostellar disks) and the physical processes (accretion, irradiation by UV and/or X-rays, excitation through slow and fast shocks) which take place. The mid-IR spectral range hosts a suite of diagnostic lines which can distinguish them. A key point is to spatially resolve the emission in the Spitzer-IRS spectra to separate extended PDR and shock emission from compact source emission associated with the circumstellar disk and jets. Methods: An optimal extraction method is used to separate both spatially unresolved (compact, up to a few hundred AU) and spatially resolved (extended, thousand AU or more) emission from the IRS spectra. The results are compared with the c2d disk sample and literature PDR and shock models to address the physical nature of the sources. Results: Both compact and extended emission features are observed. Warm (T_ex few hundred K) H2, observed through the pure rotational H2 S(0), S(1) and S(2) lines, and [S i] 25 μm emission is observed primarily in the extended component. [S i] is observed uniquely toward truly embedded sources and not toward disks. On the other hand hot (T_ex ⪆ 700 K) H2, observed primarily through the S(4) line, and [Ne ii] emission is seen mostly in the spatially unresolved component. [Fe ii] and [Si ii] lines are observed in both spatial components. Hot H2O emission is found in the spatially unresolved component of some sources. Conclusions: The observed emission on ≥1000 AU scales is characteristic of PDR emission and likely originates in the outflow cavities in the remnant envelope created by the stellar wind and jets from the embedded

  10. Combining Fits of The Optical Photometry and X-ray Spectra of the Low Mass X-ray Binary V1408 Aquilae.

    NASA Astrophysics Data System (ADS)

    Gomez, Sebastian; Mason, Paul A.; Robinson, Edward L.

    2015-01-01

    V1408 Aquilae is a binary system with a black hole primary accreting matter from a low mass secondary. We observed the system at the McDonald Observatory and collected 126 hours of high speed optical photometry on the source. We modeled the optical light curve using the XRbinary light curve synthesis software. The best fits to the optical light curve seem to suggest that the primary is a low mass black hole, however we cannot exclude some high mass solutions. Our models slightly favor a 3 solar mass primary at an inclination of about 13 degrees. In order to further constrain these parameters, and verify their validity we compared the fits of the optical light curve to fits to the X-ray spectra of the source. Using data from the Chandra Transmission Grating Catalog and Archive and the ISIS software analysis package we modeled the spectra of the source with a multi-temperature blackbody for a relativistic accretion disk around a spinning black hole and an additional photon power law component. The fits to the optical lightcurve and X-ray spectra are in agreement, from this we conclude that the case for V1408 Aql to be at a low inclination and harbor a low mass black hole is plausible.

  11. Kendrick-analogous network visualisation of ion cyclotron resonance Fourier transform mass spectra: improved options for the assignment of elemental compositions and the classification of organic molecular complexity.

    PubMed

    Tziotis, D; Hertkorn, N; Schmitt-Kopplin, Ph

    2011-01-01

    Here, we propose a novel computational and visual approach for the analysis of high field Fourier transform ion cyclotron resonance mass spectra (FTICR/MS) based on successive and multiple atomic and Kendrick analogous mass difference analyses. Compositional networks based on elemental compositions and functional networks based on selected functional groups equivalents enable improved assignment options of elemental composition and classification of organic complexity with tunable validation windows. The approach is demonstrated through the analysis of a 12T FTICR mass spectrum of an intricate water soluble extract of a secondary organic aerosol with a previously established abundance in CHNOS molecules.

  12. A mass spectrometric system for analyzing thermal desorption spectra of ion-implanted argon and cesium in tungsten. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Wood, G. M., Jr.

    1974-01-01

    A mass spectrometric system for determining the characteristics of materials used in instrumental development and aerospace applications was developed. The desorption spectra of cesium that was ion-implanted into polycrystalline tungsten and the effects on the spectra of bombardment of the tungsten by low energy (70 eV) electrons were investigated. Work function changes were measured by the retarding potential diode method. Flash desorption characteristics were observed and gas-reaction mechanisms of the surface of heated metal filaments were studied. Desorption spectra were measured by linearly increasing the sample temperature at a selected rate, the temperature cycling being generated from a ramp-driven dc power supply, with the mass spectrometer tuned to a mass number of interest. Results of the study indicate an anomolous desorption mechanism following an electron bombardment of the sample surface. The enhanced spectra are a function of the post-bombardment time and energy and are suggestive of an increased concentration of cesium atoms, up to 10 or more angstroms below the surface.

  13. Applications and limitations of constrained high-resolution peak fitting on low resolving power mass spectra from the ToF-ACSM

    NASA Astrophysics Data System (ADS)

    Timonen, Hilkka; Cubison, Mike; Aurela, Minna; Brus, David; Lihavainen, Heikki; Hillamo, Risto; Canagaratna, Manjula; Nekat, Bettina; Weller, Rolf; Worsnop, Douglas; Saarikoski, Sanna

    2016-07-01

    The applicability, methods and limitations of constrained peak fitting on mass spectra of low mass resolving power (m/Δm50 ˜ 500) recorded with a time-of-flight aerosol chemical speciation monitor (ToF-ACSM) are explored. Calibration measurements as well as ambient data are used to exemplify the methods that should be applied to maximise data quality and assess confidence in peak-fitting results. Sensitivity analyses and basic peak fit metrics such as normalised ion separation are employed to demonstrate which peak-fitting analyses commonly performed in high-resolution aerosol mass spectrometry are appropriate to perform on spectra of this resolving power. Information on aerosol sulfate, nitrate, sodium chloride, methanesulfonic acid as well as semi-volatile metal species retrieved from these methods is evaluated. The constants in a commonly used formula for the estimation of the mass concentration of hydrocarbon-like organic aerosol may be refined based on peak-fitting results. Finally, application of a recently published parameterisation for the estimation of carbon oxidation state to ToF-ACSM spectra is validated for a range of organic standards and its use demonstrated for ambient urban data.

  14. Absorption-Mode Fourier Transform Mass Spectrometry: The Effects of Apodization and Phasing on Modified Protein Spectra

    NASA Astrophysics Data System (ADS)

    Qi, Yulin; Li, Huilin; Wills, Rebecca H.; Perez-Hurtado, Pilar; Yu, Xiang; Kilgour, David P. A.; Barrow, Mark P.; Lin, Cheng; O'Connor, Peter B.

    2013-06-01

    The method of phasing broadband Fourier transform ion cyclotron resonance (FT-ICR) spectra allows plotting the spectra in the absorption-mode; this new approach significantly improves the quality of the data at no extra cost. Herein, an internal calibration method for calculating the phase function has been developed and successfully applied to the top-down spectra of modified proteins, where the peak intensities vary by 100×. The result shows that the use of absorption-mode spectra allows more peaks to be discerned within the recorded data, and this can reveal much greater information about the protein and modifications under investigation. In addition, noise and harmonic peaks can be assigned immediately in the absorption-mode.

  15. Absorption-mode Fourier transform mass spectrometry: the effects of apodization and phasing on modified protein spectra.

    PubMed

    Qi, Yulin; Li, Huilin; Wills, Rebecca H; Perez-Hurtado, Pilar; Yu, Xiang; Kilgour, David P A; Barrow, Mark P; Lin, Cheng; O'Connor, Peter B

    2013-06-01

    The method of phasing broadband Fourier transform ion cyclotron resonance (FT-ICR) spectra allows plotting the spectra in the absorption-mode; this new approach significantly improves the quality of the data at no extra cost. Herein, an internal calibration method for calculating the phase function has been developed and successfully applied to the top-down spectra of modified proteins, where the peak intensities vary by 100×. The result shows that the use of absorption-mode spectra allows more peaks to be discerned within the recorded data, and this can reveal much greater information about the protein and modifications under investigation. In addition, noise and harmonic peaks can be assigned immediately in the absorption-mode.

  16. Ion Mobility Mass Spectrometry for Ion Recovery and Clean-Up of MS and MS/MS Spectra Obtained from Low Abundance Viral Samples

    NASA Astrophysics Data System (ADS)

    Harvey, David J.; Crispin, Max; Bonomelli, Camille; Scrivens, Jim H.

    2015-07-01

    Many samples of complex mixtures of N-glycans released from small amounts of material, such as glycoproteins from viruses, present problems for mass spectrometric analysis because of the presence of contaminating material that is difficult to remove by conventional methods without involving sample loss. This study describes the use of ion mobility for extraction of glycan profiles from such samples and for obtaining clean CID spectra when targeted m/z values capture additional ions from those of the target compound. N-glycans were released enzymatically from within SDS-PAGE gels, from the representative recombinant glycoprotein, gp120 of the human immunodeficiency virus, and examined by direct infusion electrospray in negative mode followed by ion mobility with a Waters Synapt G2 mass spectrometer (Waters MS-Technologies, Manchester, UK). Clean profiles of singly, doubly, and triply charged N-glycans were obtained from samples in cases where the raw electrospray spectra displayed only a few glycan ions as the result of low sample concentration or the presence of contamination. Ion mobility also enabled uncontaminated CID spectra to be obtained from glycans when their molecular ions displayed coincidence with ions from fragments or multiply charged ions with similar m/z values. This technique proved to be invaluable for removing extraneous ions from many CID spectra. The presence of such ions often produces spectra that are difficult to interpret. Most CID spectra, even those from abundant glycan constituents, benefited from such clean-up, showing that the extra dimension provided by ion mobility was invaluable for studies of this type.

  17. Ion Mobility Mass Spectrometry for Ion Recovery and Clean-Up of MS and MS/MS Spectra Obtained from Low Abundance Viral Samples.

    PubMed

    Harvey, David J; Crispin, Max; Bonomelli, Camille; Scrivens, Jim H

    2015-10-01

    Many samples of complex mixtures of N-glycans released from small amounts of material, such as glycoproteins from viruses, present problems for mass spectrometric analysis because of the presence of contaminating material that is difficult to remove by conventional methods without involving sample loss. This study describes the use of ion mobility for extraction of glycan profiles from such samples and for obtaining clean CID spectra when targeted m/z values capture additional ions from those of the target compound. N-glycans were released enzymatically from within SDS-PAGE gels, from the representative recombinant glycoprotein, gp120 of the human immunodeficiency virus, and examined by direct infusion electrospray in negative mode followed by ion mobility with a Waters Synapt G2 mass spectrometer (Waters MS-Technologies, Manchester, UK). Clean profiles of singly, doubly, and triply charged N-glycans were obtained from samples in cases where the raw electrospray spectra displayed only a few glycan ions as the result of low sample concentration or the presence of contamination. Ion mobility also enabled uncontaminated CID spectra to be obtained from glycans when their molecular ions displayed coincidence with ions from fragments or multiply charged ions with similar m/z values. This technique proved to be invaluable for removing extraneous ions from many CID spectra. The presence of such ions often produces spectra that are difficult to interpret. Most CID spectra, even those from abundant glycan constituents, benefited from such clean-up, showing that the extra dimension provided by ion mobility was invaluable for studies of this type.

  18. Twelve million resolving power on 4.7 T Fourier transform ion cyclotron resonance instrument with dynamically harmonized cell--observation of fine structure in peptide mass spectra.

    PubMed

    Popov, Igor A; Nagornov, Konstantin; Vladimirov, Gleb N; Kostyukevich, Yury I; Nikolaev, Eugene N

    2014-05-01

    Resolving power of about 12,000 000 at m/z 675 has been achieved on low field homogeneity 4.7 T magnet using a dynamically harmonized Fourier transform ion cyclotron resonance (FT ICR) cell. Mass spectra of the fine structure of the isotopic distribution of a peptide were obtained and strong discrimination of small intensity peaks was observed in case of resonance excitation of the ions of the whole isotopic cluster to the same cyclotron radius. The absence of some peaks from the mass spectra of the fine structure was explained basing on results of computer simulations showing strong ion cloud interactions, which cause the coalescence of peaks with m/z close to that of the highest magnitude peak. The way to prevent peak discrimination is to excite ion clouds of different m/z to different cyclotron radii, which was demonstrated and investigated both experimentally and by computer simulations.

  19. Measurement of Dielectron Invariant Mass Spectra in Au + Au Collisions at p sNN = 200GeV with HBD in PHENIX

    NASA Astrophysics Data System (ADS)

    Sun, Jiayin

    Dileptons are emitted throughout the entire space-time evolution of heavy ion collisions. Being colorless, these electromagnetic probes do not participate in the final-state strong interactions during the passage through the hot medium, and retain the information on the conditions of their creation. This characteristic renders them valuable tools for studying the properties of the Quark Gluon Plasma created during ultra-relativistic heavy ion collisions. The invariant mass spectra of dileptons contain a wealth of information on every stage of the evolution of heavy ion collisions. At low mass, dilepton spectra consist mainly of light meson decays. The medium modification of the light vector mesons gives insight on the chiral symmetry restoration in heavy ion collisions. At intermediate and high mass, there are significant contributions from charm and bottom, with a minor contribution from QGP thermal radiation. The region was utilized to measure cross sections of open charm and open bottom, as well as quarkonium suppression as demonstrated by PHENIX. An earlier PHENIX measurement of dielectron spectra in heavy ion collisions, using data taken in 2004, shows significant deviations from the hadronic decay expectations. The measurement, however, suffered from an unfavorable signal to background ratio. Random combination of electron-positron pairs from unrelated sources, mostly Dalitz decay of pi0 and external conversion of decay photon to electrons, is the main contributor to the background. Mis-identified hadrons are another major background source. To improve the situation, the Hadron Blind Detector (HBD), a windowless proximity focusing Cerenkov detector, is designed to reduce this background by identifying electron tracks from photon conversions and pi. 0 Dalitzdecays. The detector has been installed and operated in PHENIX in 2009 and 2010, where reference p+p and Au+Au data sets were successfully taken. We will present the dielectron results from the analysis of

  20. Computer programs for the interpretation of low resolution mass spectra: Program for calculation of molecular isotopic distribution and program for assignment of molecular formulas

    NASA Technical Reports Server (NTRS)

    Miller, R. A.; Kohl, F. J.

    1977-01-01

    Two FORTRAN computer programs for the interpretation of low resolution mass spectra were prepared and tested. One is for the calculation of the molecular isotopic distribution of any species from stored elemental distributions. The program requires only the input of the molecular formula and was designed for compatability with any computer system. The other program is for the determination of all possible combinations of atoms (and radicals) which may form an ion having a particular integer mass. It also uses a simplified input scheme and was designed for compatability with any system.

  1. Time of flight mass spectra of ions in plasmas produced by hypervelocity impacts of organic and mineralogical microparticles on a cosmic dust analyser

    NASA Astrophysics Data System (ADS)

    Goldsworthy, B. J.; Burchell, M. J.; Cole, M. J.; Armes, S. P.; Khan, M. A.; Lascelles, S. F.; Green, S. F.; McDonnell, J. A. M.; Srama, R.; Bigger, S. W.

    2003-10-01

    The ionic plasma produced by a hypervelocity particle impact can be analysed to determine compositional information for the original particle by using a time-of-flight mass spectrometer. Such methods have been adopted on interplanetary dust detectors to perform in-situ analyses of encountered grains, for example, the Cassini Cosmic Dust Analyser (CDA). In order to more fully understand the data returned by such instruments, it is necessary to study their response to impacts in the laboratory. Accordingly, data are shown here for the mass spectra of ionic plasmas, produced through the acceleration of microparticles via a 2 MV van de Graaff accelerator and their impact on a dimensionally correct CDA model with a rhodium target. The microparticle dusts examined have three different chemical compositions: metal (iron), organic (polypyrrole and polystyrene latex) and mineral (aluminosilicate clay). These microparticles have mean diameters in the range 0.1 to 1.6 mu m and their velocities range from 1-50 km s-1. They thus cover a wide range of compositions, sizes and speeds expected for dust particles encountered by spacecraft in the Solar System. The advent of new low-density, microparticles with highly controllable attributes (composition, size) has enabled a number of new investigations in this area. The key is the use of a conducting polymer, either as the particle itself or as a thin overlayer on organic (or inorganic) core particles. This conductive coating permits efficient electrostatic charging and acceleration. Here, we examine how the projectile's chemical composition influences the ionic plasma produced after the hypervelocity impact. This study thus extends our understanding of impact plasma formation and detection. The ionization yield normalized to particle mass was found to depend on impact speed to the power (3.4 +/- 0.1) for iron and (2.9 +/- 0.1) for polypyrrole coated polystyrene and aluminosilicate clay. The ioization signal rise time was found to

  2. Charge Prediction Machine: A tool for inferring precursor charge states of Electron Transfer Dissociation tandem mass spectra

    PubMed Central

    Carvalho, Paulo C; Cociorva, Daniel; Wong, Catherine; Carvalho, Maria da Gloria da C; Barbosa, Valmir C; Yates, John R

    2010-01-01

    Electron Transfer Dissociation (ETD) can dissociate highly charged ions. Efficient analysis of ions dissociated with ETD requires accurate determination of charge states for calculation of molecular weight. We created an algorithm to assign the charge state of ions often used for ETD. The program, Charge Prediction Machine (CPM), uses Bayesian decision theory to account for different charge reduction processes encountered in ETD, and can also handle multiplex spectra. CPM correctly assigned charge states to 98% of the 13,097 MS2 spectra from a combined dataset of four experiments. In a comparison between CPM and a competing program, Charger (ThermoFisher), CPM produced half the mistakes. PMID:19203245

  3. Relative mass defect filtering of high-resolution mass spectra for exploring minor selenium volatiles in selenium-enriched green onions.

    PubMed

    Shah, Monika; Meija, Juris; Caruso, Joseph A

    2007-02-01

    In this study, the presence of minor Se-containing volatiles in Se-enriched green onions (Allium fistulosum) was investigated using the combination of high-resolution mass spectrometry, inductively coupled plasma mass spectrometry, and a simple relative mass defect-based algorithm to aid trace level analysis of unknown components. This confirmed the structures of volatiles reported previously, along with several unreported small molecular weight Se-containing volatiles from plants, such as MeSeSeSMe. This data analysis technique was also useful to link the results obtained from molecular and elemental mass spectrometry thus aiding in the search for new trace level Se-containing volatiles. PMID:17263309

  4. Typical ultraviolet spectra in combination with diagnostic mass fragmentation analysis for the rapid and comprehensive profiling of chlorogenic acids in the buds of Lonicera macranthoides.

    PubMed

    Zhang, Shui-Han; Hu, Xin; Shi, Shu-Yun; Huang, Lu-Qi; Chen, Wei; Chen, Lin; Cai, Ping

    2016-05-01

    A major challenge of profiling chlorogenic acids (CGA) in natural products is to effectively detect unknown or minor isomeric compounds. Here, we developed an effective strategy, typical ultraviolet (UV) spectra in combination with diagnostic mass fragmentation analysis based on HPLC-DAD-QTOF-MS/MS, to comprehensively profile CGA in the buds of Lonicera macranthoides. First, three CGA UV patterns were obtained by UV spectra screening. Second, 13 types of CGA classified by molecular weights were found by thorough analysis of CGA peaks using high-resolution MS. Third, selected ion monitoring (SIM) was carried out for each type of CGA to avoid overlooking of minor ones. Fourth, MS/MS spectra of each CGA were investigated. Then 70 CGA were identified by matching their UV spectra, accurate mass signals and fragmentation patterns with standards or previously reported compounds, including six caffeoylquinic acids (CQA), six diCQA, one triCQA, three caffeoylshikimic acids (CSA), six diCSA, one triCSA, three p-coumaroylquinic acids (pCoQA), four p-coumaroylcaffeoylquinic acids (pCoCQA), four feruloylquinic acids (FQA), five methyl caffeoylquinates (MCQ), three ethyl caffeoylquinates (ECQ), three dimethoxycinnamoylquinic acids (DQA), six caffeoylferuloylquinic acids (CFQA), six methyl dicaffeoylquinates (MdiCQ), four FQA glycosides (FQAG), six MCQ glycosides (MCQG), and three ethyl dicaffeoylquinates (EdiCQ). Forty-five of them were discovered from Lonicera species for the first time, and it is noted that CGA profiles were investigated for the first time in L. macranthoides. Results indicated that the developed method was a useful approach to explore unknown and minor isomeric compounds from complex natural products. PMID:26970751

  5. Reduction in database search space by utilization of amino acid composition information from electron transfer dissociation and higher-energy collisional dissociation mass spectra.

    PubMed

    Hansen, Thomas A; Kryuchkov, Fedor; Kjeldsen, Frank

    2012-08-01

    With high-mass accuracy and consecutively obtained electron transfer dissociation (ETD) and higher-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS), reliable (≥97%) and sensitive fragment ions have been extracted for identification of specific amino acid residues in peptide sequences. The analytical benefit of these specific amino acid composition (AAC) ions is to restrict the database search space and provide identification of peptides with higher confidence and reduced false negative rates. The 6706 uniquely identified peptide sequences determined with a conservative Mascot score of >30 were used to characterize the AAC ions. The loss of amino acid side chains (small neutral losses, SNLs) from the charge reduced peptide radical cations was studied using ETD. Complementary AAC information from HCD spectra was provided by immonium ions. From the ETD/HCD mass spectra, 5162 and 6720 reliable SNLs and immonium ions were successfully extracted, respectively. Automated application of the AAC information during database searching resulted in an average 3.5-fold higher confidence level of peptide identification. In addition, 4% and 28% more peptides were identified above the significance level in a standard and extended search space, respectively.

  6. Free electron laser-Fourier transform ion cyclotron resonance mass spectrometry facility for obtaining infrared multiphoton dissociation spectra of gaseous ions

    SciTech Connect

    Valle, Jose J.; Eyler, John R.; Oomens, Jos; Moore, David T.; Meer, A.F.G. van der; Helden, Gert von; Meijer, Gerard; Hendrickson, Christopher L.; Marshall, Alan G.; Blakney, Gregory T.

    2005-02-01

    A Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer has been installed at a free electron laser (FEL) facility to obtain infrared absorption spectra of gas phase ions by infrared multiple photon dissociation (IRMPD). The FEL provides continuously tunable infrared radiation over a broad range of the infrared spectrum, and the FT-ICR mass spectrometer, utilizing a 4.7 Tesla superconducting magnet, permits facile formation, isolation, trapping, and high-mass resolution detection of a wide range of ion classes. A description of the instrumentation and experimental parameters for these experiments is presented along with preliminary IRMPD spectra of the singly-charged chromium-bound dimer of diethyl ether (Cr(C{sub 4}H{sub 10}O){sub 2}{sup +}) and the fluorene molecular ion (C{sub 13}H{sub 10}{sup +}). Also presented is a brief comparison of the fluorene cation spectrum obtained by the FT-ICR-FEL with an earlier spectrum recorded using a quadrupole ion trap (QIT)

  7. CONFIRMATION OF ENHANCED DWARF-SENSITIVE ABSORPTION FEATURES IN THE SPECTRA OF MASSIVE ELLIPTICAL GALAXIES: FURTHER EVIDENCE FOR A NON-UNIVERSAL INITIAL MASS FUNCTION

    SciTech Connect

    Van Dokkum, Pieter G.; Conroy, Charlie

    2011-07-01

    We recently found that massive cluster elliptical galaxies have strong Na I {lambda}8183, 8195 and FeH {lambda}9916 Wing-Ford band absorption, indicating the presence of a very large population of stars with masses {approx}< 0.3 M{sub sun}. Here we test this result by comparing the elliptical galaxy spectra to those of luminous globular clusters associated with M31. These globular clusters have similar metallicities, abundance ratios, and ages as massive elliptical galaxies but their low dynamical mass-to-light ratios rule out steep stellar initial mass functions (IMFs). From high-quality Keck spectra we find that the dwarf-sensitive absorption lines in globular clusters are significantly weaker than in elliptical galaxies and consistent with normal IMFs. The differences in the Na I and Wing-Ford indices are 0.027 {+-} 0.007 mag and 0.017 {+-} 0.006 mag, respectively. We directly compare the two classes of objects by subtracting the averaged globular cluster spectrum from the averaged elliptical galaxy spectrum. The difference spectrum is well fit by the difference between a stellar population synthesis model with a bottom-heavy IMF and one with a bottom-light IMF. We speculate that the slope of the IMF may vary with velocity dispersion, although it is not yet clear what physical mechanism would be responsible for such a relation.

  8. A thermal model of Rosetta/ROSINA/DFMS to assess the effects of solar illumination and thermal inertia of the mass spectrometer on mass spectra at 67P/Churyumov-Gerasimenko

    NASA Astrophysics Data System (ADS)

    De Keyser, Johan; Gibbons, Andrew; Neefs, Eddy; Equeter, Eddy; Dhooghe, Frederik; Maggiolo, Romain; Cessateur, Gaël; Gunell, Herbert; Altwegg, Kathrin; Berthelier, Jean-Jacques; Briois, Christelle; Calmonte, Ursina; Combi, Michael R.; Fiethe, Björn; Fuselier, Stephen; Gombosi, Tamas; Hässig, Myrttha; Le Roy, Léna; Rubin, Martin; Sémon, Thierry

    2016-04-01

    The coma composition of comet 67P/Churyumov-Gerasimenko is being analysed in detail with the high mass resolution Double Focussing Mass Spectrometer (DFMS) that is part of the ROSINA instrument suite on board of the Rosetta spacecraft. The Rosetta spacecraft - and DFMS in particular - experiences changing behaviour as the temperature varies with illumination and distance from the Sun. This contribution highlights these changes and their practical consequences for the interpretation of the DFMS mass spectra. A thermal model is presented that addresses thermal behaviour on a long time scale, related to instrument illumination and thermal gradients inside DFMS, and on a short time scale, related to transients after on/off cycling of the instrument and thermal inertia. Both issues adversely affect the problem of establishing a proper instrument mass calibration.

  9. Extreme ultraviolet ionization of pure He nanodroplets: mass-correlated photoelectron imaging, Penning ionization, and electron energy-loss spectra.

    PubMed

    Buchta, D; Krishnan, S R; Brauer, N B; Drabbels, M; O'Keeffe, P; Devetta, M; Di Fraia, M; Callegari, C; Richter, R; Coreno, M; Prince, K C; Stienkemeier, F; Ullrich, J; Moshammer, R; Mudrich, M

    2013-08-28

    The ionization dynamics of pure He nanodroplets irradiated by Extreme ultraviolet radiation is studied using Velocity-Map Imaging PhotoElectron-PhotoIon COincidence spectroscopy. We present photoelectron energy spectra and angular distributions measured in coincidence with the most abundant ions He(+), He2(+), and He3(+). Surprisingly, below the autoionization threshold of He droplets, we find indications for multiple excitation and subsequent ionization of the droplets by a Penning-like process. At high photon energies we observe inelastic collisions of photoelectrons with the surrounding He atoms in the droplets.

  10. Effect of the reducing-terminal substituents on the high energy collision-induced dissociation matrix-assisted laser desorption/ionization mass spectra of oligosaccharides.

    PubMed

    Küster, B; Naven, T J; Harvey, D J

    1996-01-01

    High-energy collision-induced dissociation (CID) matrix-assisted laser desorption/ionization mass spectra of N-linked oligosaccharides bearing different, commonly encountered, reducing terminal modifications (hydroxyl, 2-aminobenzamide, asparagine and a tetrapeptide) were recorded on a magnetic sector instrument equipped with an orthogonal-acceleration time-of-flight (OA-TOF) analyser. All the compounds formed abundant molecular (MNa+) and fragment ions, the latter corresponding to glycosidic and cross-ring cleavages as well as to internal fragment ions, all of which provided much insight into the oligosaccharide structure. The nature of the modification considerably influenced the CID behaviour. The strongest and most complete series of glycosidic cleavage ions (mainly Y and B--Domon and Costello nomenclature) was formed by the underivatized oligosaccharide whereas most cross-ring fragment ions, diagnostic of linkage, were found in the spectra of the glycopeptides. A-type cross-ring cleavage ions were particularly abundant in the spectrum of the asparagine derivative. Reductive amination using 2-aminobenzamide resulted in an opened reducing-terminal sugar ring and suppression of the cross-ring fragment ions carrying information associated with that ring. This information was present in the spectra of the free carbohydrate and the peptide derivatives. PMID:8914337

  11. Secondary ion emission from CO2-H2O ice irradiated by energetic heavy ions: Part I. Measurement of the mass spectra

    NASA Astrophysics Data System (ADS)

    Farenzena, L. S.; Collado, V. M.; Ponciano, C. R.; da Silveira, E. F.; Wien, K.

    2005-05-01

    Secondary ion mass spectrometry is used to investigate ion emission from a frozen-gas mixture (T = 80-90 K) of CO2 and H2O bombarded by MeV nitrogen ions and by 252Cf fission fragments (FF). The aim of the experiments is to produce organic molecules in the highly excited material around the nuclear track and to detect them in the flux of sputtered particles. Such sputter processes are known to occur at the icy surfaces of planetary or interstellar objects. Time-of-flight (TOF) mass spectrometry is employed to identify the desorbed ions. Mass spectra of positive and negative ions were taken for several molecular H2O/CO2 ratios. In special, positive ions induced by MeV nitrogen beam were analyzed for 9 and 18% H2O concentrations of the CO2-H2O ice and negative ions for ~5% H2O. The ion peaks are separated to generate exclusive the spectra of CO2 specific ions, H2O specific ions and hybrid molecular ions, the latter ones corresponding to ions that contain mostly H and C atoms. In the mass range from 10 to 320 u, the latter exhibits 35 positive and 58 negative ions. The total yield of the positive ions is 0.35 and 0.57 ions/impact, respectively, and of negative ions 0.066 ions/impact. Unexpected effects of secondary ion sputtering yields on H2O/CO2 ratio are attributed to the influence of water molecules concentration on the ionization process.

  12. Lily Pad Spectra

    NASA Technical Reports Server (NTRS)

    2004-01-01

    The color image on the lower left from the panoramic camera on the Mars Exploration Rover Opportunity shows the 'Lily Pad' bounce-mark area at Meridiani Planum, Mars. This image was acquired on the 3rd sol, or martian day, of Opportunity's mission (Jan.26, 2004). The upper left image is a monochrome (single filter) image from the rover's panoramic camera, showing regions from which spectra were extracted from the 'Lily Pad' area. As noted by the line graph on the right, the green spectra is from the undisturbed surface and the red spectra is from the airbag bounce mark.

  13. Retention indices, relative response factors, and mass spectra of trifluoroethyl and heptafluorobutyl esters of carboxylic acids determined by capillary GC/MS

    SciTech Connect

    Yu, S.K.-T.; Vrana, R.P.; Green, J.B.

    1990-11-01

    The GC/MS characteristics of carboxylic acid esters prepared from fluorine-containing alcohols were compared to those of methyl esters. The GC retention of 2,2,2-trifluoroethyl (TFE) esters was less than, and 2,2,3,3,4,4,4-heptafluoro-1-butyl (HFB) esters approximately equivalent to that of methyl esters. The peak shape of both TFE and HFB esters was slightly superior to that of methyl esters. Mass spectra of TFE and HFB aliphatic esters show significantly more intense molecular and key fragment ions than those of methyl esters. Also, owing to their significantly higher molecular weights, TFE or HFB ester molecular ions and most fragment ions of interest occur at significantly higher m/z values than most potential interfering ions. The GC retention indices, relative GC/MS total ion current response factors, and 70 eV electron impact mass spectra of about 70 TFE and 70 HFB carboxylic acid esters are reported. Results from analysis of a TFE/HFB esterified petroleum carboxylic acid concentrate are discussed in detail. 26 refs., 17 figs., 3 tabs.

  14. Effect of Vaporizer Temperature on Ambient Non-Refractory Submicron Aerosol Composition and Mass Spectra Measured by the Aerosol Mass Spectrometer

    EPA Science Inventory

    Aerodyne Aerosol Mass Spectrometers (AMS) are routinely operated with a constant vaporizer temperature (Tvap) of 600oC in order to facilitate quantitative detection of non-refractory submicron (NR-PM1) species. By analogy with other thermal desorption instrument...

  15. Modified Miniature Thomson-Type Analyzer For Measurements Of Mass- and Energy-Spectra Of Ions Within Plasma Facilities

    SciTech Connect

    Czaus, K.; Malinowski, K.; Sadowski, M. J.; Skladnik-Sadowska, E.

    2008-03-19

    The paper describes important improvements in the construction and operation of a miniature mass- and energy-analyzer of the Thomson type, which was developed especially for measurements of ions inside vacuum experimental chambers. The described analyzer constitutes a modified and improved version of the prototype miniature mass-spectrometer, which was designed several years ago. The paper describes experimental tests of the modified analyzer, which were carried out in the RPI-IBIS facility equipped with a multi-rod plasma injector. Results of the detailed measurements of energy distributions of protons and deuterons (from deuterium discharges) within the energy range from about 20 keV to about 300 keV are also presented.

  16. VizieR Online Data Catalog: Spectra of low-mass stars in Upper Sco (Lodieu+, 2011)

    NASA Astrophysics Data System (ADS)

    Lodieu, N.; Dobbie, P. D.; Hambly, N. C.

    2010-11-01

    Coordinates (J2000), ZYJHK photometry from the UKIDSS Galactic Clusters Survey, and proper motions derived from the UKIDSS/2MASS cross-match (in arcsec/yr) of stars in the AAOmega field-of-view ordered by increasing Z magnitude. The last column provides a tentative estimate of the spectral type. Data obtained with the AAOmega spectrograph on the Anglo-Australian telescope in May 2007. (4 data files).

  17. An evaluation of the impact of urban air pollution on paint dosimeters by tracking changes in the lipid MALDI-TOF mass spectra profile.

    PubMed

    Herrera, A; Navas, N; Cardell, C

    2016-08-01

    We evaluated the impact of urban air pollution on egg yolk tempera paint dosimeters (binary mixture samples made with historic artist´s blue, red and white pigments) by tracking changes over time in their lipid matrix-assisted laser desorption ionization time-of-flight mass spectra (MALDI-TOF-MS) profiles. We studied triacylglycerols (TGs), phospholipids (PLs) and their oxidation by-products from paint dosimeters that had been exposed outdoors for six months to the polluted atmosphere in the city center of Granada (Spain). Four types of chickens' eggs were also analyzed to find out whether their lipid mass spectra (lipid fingerprints) varied significantly. The ultimate goal of this research is to provide a precise analytical protocol to show whether the changes in the egg yolk identified in paint dosimeters are due to pigment-binder interactions. The Bligh-Dyer (BD) method was optimized for the extraction of the lipids. This innovative procedure included a washing-step prior to the mass spectrometric analysis, which proved crucial for obtaining higher quality lipid fingerprints. A novel interpretation of the results is proposed by applying the BD method, which suggests that transesterification processes occurred in the lipid fractions that were catalyzed by the pigments in the paint dosimeters. In blank dosimeters specific ions produced by oxidative cleavage of PLs and/or TGs may be used as markers of the presence of egg yolk binders. The composition and structure of the specific lipid compounds are also tentatively proposed. In aged dosimeters the intact content of the TGs and PLs decreased; however, we propose that short-chain oxidative products arising from TGs and PLs are present in all the samples, except for the white lead based dosimeter. We end with a new explanation as to why this dosimeter behaves differently from the others.

  18. An evaluation of the impact of urban air pollution on paint dosimeters by tracking changes in the lipid MALDI-TOF mass spectra profile.

    PubMed

    Herrera, A; Navas, N; Cardell, C

    2016-08-01

    We evaluated the impact of urban air pollution on egg yolk tempera paint dosimeters (binary mixture samples made with historic artist´s blue, red and white pigments) by tracking changes over time in their lipid matrix-assisted laser desorption ionization time-of-flight mass spectra (MALDI-TOF-MS) profiles. We studied triacylglycerols (TGs), phospholipids (PLs) and their oxidation by-products from paint dosimeters that had been exposed outdoors for six months to the polluted atmosphere in the city center of Granada (Spain). Four types of chickens' eggs were also analyzed to find out whether their lipid mass spectra (lipid fingerprints) varied significantly. The ultimate goal of this research is to provide a precise analytical protocol to show whether the changes in the egg yolk identified in paint dosimeters are due to pigment-binder interactions. The Bligh-Dyer (BD) method was optimized for the extraction of the lipids. This innovative procedure included a washing-step prior to the mass spectrometric analysis, which proved crucial for obtaining higher quality lipid fingerprints. A novel interpretation of the results is proposed by applying the BD method, which suggests that transesterification processes occurred in the lipid fractions that were catalyzed by the pigments in the paint dosimeters. In blank dosimeters specific ions produced by oxidative cleavage of PLs and/or TGs may be used as markers of the presence of egg yolk binders. The composition and structure of the specific lipid compounds are also tentatively proposed. In aged dosimeters the intact content of the TGs and PLs decreased; however, we propose that short-chain oxidative products arising from TGs and PLs are present in all the samples, except for the white lead based dosimeter. We end with a new explanation as to why this dosimeter behaves differently from the others. PMID:27216656

  19. Oil spill source identification by principal component analysis of electrospray ionization Fourier transform ion cyclotron resonance mass spectra.

    PubMed

    Corilo, Yuri E; Podgorski, David C; McKenna, Amy M; Lemkau, Karin L; Reddy, Christopher M; Marshall, Alan G; Rodgers, Ryan P

    2013-10-01

    One fundamental challenge with either acute or chronic oil spills is to identify the source, especially in highly polluted areas, near natural oil seeps, when the source contains more than one petroleum product or when extensive weathering has occurred. Here we focus on heavy fuel oil that spilled (~200,000 L) from two suspected fuel tanks that were ruptured on the motor vessel (M/V) Cosco Busan when it struck the San Francisco-Oakland Bay Bridge in November 2007. We highlight the utility of principal component analysis (PCA) of elemental composition data obtained by high resolution FT-ICR mass spectrometry to correctly identify the source of environmental contamination caused by the unintended release of heavy fuel oil (HFO). Using ultrahigh resolution electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry, we uniquely assigned thousands of elemental compositions of heteroatom-containing species in neat samples from both tanks and then applied principal component analysis. The components were based on double bond equivalents for constituents of elemental composition, CcHhN1S1. To determine if the fidelity of our source identification was affected by weathering, field samples were collected at various intervals up to two years after the spill. We are able to identify a suite of polar petroleum markers that are environmentally persistent, enabling us to confidently identify that only one tank was the source of the spilled oil: in fact, a single principal component could account for 98% of the variance. Although identification is unaffected by the presence of higher polarity, petrogenic oxidation (weathering) products, future studies may require removal of such species by anion exchange chromatography prior to mass spectral analysis due to their preferential ionization by ESI.

  20. Approach toward minimizing chemical interference in FAB mass spectra: the development and application of thermally - assisted FAB

    SciTech Connect

    Ackermann, B.L.

    1987-01-01

    Interferences with fast atom bombardment (FAB) mass spectrometry can be classified into two major categories. The first includes impurities which remain after analyte isolation/purification, and is especially problematic in samples of biological origin. The second type of chemical interference originates from the matrix used for FAB. An example of the first type, also known as sample-related interference, is presented in the context of the analysis of the urinary metabolites of the analgesic acetaminophen by means of the off-line combination of reverse phase HPLC and FAB. Recommendations are made for efficient use of these two methods with specific regard to minimizing chemical interferences. In addition, a method for calculating analyte signal to background (S/B) values is introduced as a means of evaluating the quality of the FAB mass spectrum. A method known as thermally-assisted FAB (TA-FAB) is introduced as a means of minimizing matrix-related background. Success to date has been achieved using aqueous saccharide solutions as TA-FAB matrices. Several important improvements to FAB result from thermal control of the matrix including a selection against matrix background, and the possibility of valid background subtraction. The development of TA-FAB is described in the context of applications of the technique to the analysis of several representative nonvolatile biomolecules including a series of cyclic tetrapeptide mycotoxins. In the final section, the hypothesis of ternary perculation (TP) is submitted to account for behavior observed during TA-FAB.

  1. Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification

    PubMed Central

    McAlister, Graeme C.; Phanstiel, Doug; Wenger, Craig D.; Lee, M. Violet; Coon, Joshua J.

    2009-01-01

    Using a newly developed dual-cell quadrupole linear ion trap-orbitrap hybrid mass spectrometer (dcQLT-orbitrap), we demonstrate the utility of collecting high-resolution tandem mass spectral data for large-scale shotgun proteomics. Multiple nanoLC-MS/MS experiments on both an older generation quadrupole linear ion trap-orbitrap hybrid (QLT-orbitrap) and the dcQLT-orbitrap, using both resonant-excitation CAD and beam-type CAD (HCD) were performed. Resulting from various technological advances (e.g., a stacked ring ion guide AP inlet, a dual cell QLT, etc.), the dcQLT-orbitrap exhibited increased duty cycle (~1.5–2×) and sensitivity for both CAD (ion trap detection) and HCD (orbitrap detection) methods. As compared to the older system, the dcQLT-orbitrap produced significantly more unique peptide identification for both methods (~30% improvement for CAD and ~115% improvement for HCD). The sizeable improvement of the HCD method on the dcQLT-orbitrap system, outperforms the current standard method of CAD with ion trap detection for large-scale analysis. Finally, we demonstrate that the increased HCD performance translates to a direct and substantial improvement in protein quantitation precision using isobaric tags. PMID:19938823

  2. Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides.

    PubMed

    MacCoss, Michael J; Wu, Christine C; Matthews, Dwight E; Yates, John R

    2005-12-01

    Stable isotope-enriched molecules are used as internal standards and as tracers of in vivo substrate metabolism. The accurate conversion of measured ratios in the mass spectrometer to mole ratios is complicated because a polyatomic molecule containing enriched atoms will result in a combinatorial distribution of isotopomers depending on the enrichment and number of "labeled" atoms. This effect could potentially cause a large error in the mole ratio measurement depending on which isotope peak or peaks were used to determine the ratio. We report a computational method that predicts isotope distributions over a range of enrichments and compares the predicted distributions to experimental peptide isotope distributions obtained by Fourier transform ion cyclotron resonance mass spectrometry. Our approach is accurate with measured enrichments within 1.5% of expected isotope distributions. The method is also precise with 4.9, 2.0, and 0.8% relative standard deviations for peptides containing 59, 79, and 99 atom % excess (15)N, respectively. The approach is automated making isotope enrichment calculations possible for thousands of peptides in a single muLC-FTICR-MS experiment.

  3. Estimation of Mass-Loss Rates from Emission Line Profiles in the UV Spectra of Cool Stars

    NASA Technical Reports Server (NTRS)

    Carpenter, K. G.; Robinson, R. D.; Harper, G. M.

    1999-01-01

    The photon-scattering winds of cool, low-gravity stars (K-M giants and supergiants) produce absorption features in the strong chromospheric emission lines. This provides us with an opportunity to assess important parameters of the wind, including flow and turbulent velocities, the optical depth of the wind above the region of photon creation, and the star's mass-loss rate. We have used the Lamers et al. Sobolev with Exact Integration (SEI) radiative transfer code along with simple models of the outer atmospheric structure to compute synthetic line profiles for comparison with the observed line profiles. The SEI code has the advantage of being computationally fast and allows a great number of possible wind models to be examined. We therefore use it here to obtain initial first-order estimates of the wind parameters. More sophisticated, but more time-consuming and resource intensive calculations will be performed at a later date, using the SEI-deduced wind parameters as a starting point. A comparison of the profiles over a range of wind velocity laws, turbulence values, and line opacities allows us to constrain the wind parameters, and to estimate the mass-loss rates. We have applied this analysis technique (using lines of Mg II, 0 I, and Fe II) so far to four stars: the normal K5-giant alpha Tau, the hybrid K-giant gamma Dra, the K5 supergiant lambda Vel, and the M-giant gamma Cru. We present in this paper a description of the technique, including the assumptions which go into its use, an assessment of its robustness, and the results of our analysis.

  4. Differentiation of Microbial Species and Strains in Coculture Biofilms by Multivariate Analysis of Laser Desorption Postionization Mass Spectra

    PubMed Central

    Bhardwaj, Chhavi; Cui, Yang; Hofstetter, Theresa; Liu, Suet Yi; Bernstein, Hans C.; Carlson, Ross P.; Ahmed, Musahid; Hanley, Luke

    2013-01-01

    7.87 to 10.5 eV vacuum ultraviolet (VUV) photon energies were used in laser desorption postionization mass spectrometry (LDPI-MS) to analyze biofilms comprised of binary cultures of interacting microorganisms. The effect of photon energy was examined using both tunable synchrotron and laser sources of VUV radiation. Principal components analysis (PCA) was applied to the MS data to differentiate species in Escherichia coli-Saccharomyces cerevisiae coculture biofilms. PCA of LDPI-MS also differentiated individual E. coli strains in a biofilm comprised of two interacting gene deletion strains, even though these strains differed from the wild type K-12 strain by no more than four gene deletions each out of approximately 2000 genes. PCA treatment of 7.87 eV LDPI-MS data separated the E. coli strains into three distinct groups, two “pure” groups, and a mixed region. Furthermore, the “pure” regions of the E. coli cocultures showed greater variance by PCA at 7.87 eV photon energies compared to 10.5 eV radiation. This is consistent with the expectation that the 7.87 eV photoionization selects a subset of low ionization energy analytes while 10.5 eV is more inclusive, detecting a wider range of analytes. These two VUV photon energies therefore give different spreads via PCA and their respective use in LDPI-MS constitute an additional experimental parameter to differentiate strains and species. PMID:24067765

  5. Digital Imaging Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Bamberger, Casimir; Renz, Uwe; Bamberger, Andreas

    2011-06-01

    Methods to visualize the two-dimensional (2D) distribution of molecules by mass spectrometric imaging evolve rapidly and yield novel applications in biology, medicine, and material surface sciences. Most mass spectrometric imagers acquire high mass resolution spectra spot-by-spot and thereby scan the object's surface. Thus, imaging is slow and image reconstruction remains cumbersome. Here we describe an imaging mass spectrometer that exploits the true imaging capabilities by ion optical means for the time of flight mass separation. The mass spectrometer is equipped with the ASIC Timepix chip as an array detector to acquire the position, mass, and intensity of ions that are imaged by matrix-assisted laser desorption/ionization (MALDI) directly from the target sample onto the detector. This imaging mass spectrometer has a spatial resolving power at the specimen of (84 ± 35) μm with a mass resolution of 45 and locates atoms or organic compounds on a surface area up to ~2 cm2. Extended laser spots of ~5 mm2 on structured specimens allows parallel imaging of selected masses. The digital imaging mass spectrometer proves high hit-multiplicity, straightforward image reconstruction, and potential for high-speed readout at 4 kHz or more. This device demonstrates a simple way of true image acquisition like a digital photographic camera. The technology may enable a fast analysis of biomolecular samples in near future.

  6. FEEDBACK FROM HIGH-MASS X-RAY BINARIES ON THE HIGH-REDSHIFT INTERGALACTIC MEDIUM: MODEL SPECTRA

    SciTech Connect

    Power, Chris; James, Gillian; Wynn, Graham; Combet, Celine

    2013-02-10

    Massive stars at redshifts z {approx}> 6 are predicted to have played a pivotal role in cosmological reionization as luminous sources of ultraviolet (UV) photons. However, the remnants of these massive stars could be equally important as X-ray-luminous (L{sub X} {approx} 10{sup 38} erg s{sup -1}) high-mass X-ray binaries (HMXBs). Because the absorption cross section of neutral hydrogen decreases sharply with photon energy ({sigma}{proportional_to}E {sup -3}), X-rays can escape more freely than UV photons from the star-forming regions in which they are produced, allowing HMXBs to make a potentially significant contribution to the ionizing X-ray background during reionization. In this paper, we explore the ionizing power of HMXBs at redshifts z {approx}> 6 using a Monte Carlo model for a coeval stellar population of main-sequence stars and HMXBs. Using the archetypal Galactic HMXB Cygnus X-1 as our template, we propose a composite HMXB spectral energy distribution consisting of blackbody and power-law components, whose contributions depend on the accretion state of the system. We determine the time-dependent ionizing power of a combined population of UV-luminous stars and X-ray-luminous HMXBs and deduce fitting formulae for the boost in the population's ionizing power arising from HMXBs; these fits allow for simple implementation of HMXB feedback in numerical simulations. Based on this analysis, we estimate the contribution of high-redshift HMXBs to the present-day soft X-ray background, and we show that it is a factor of {approx}100-1000 smaller than the observed limit. Finally, we discuss the implications of our results for the role of HMXBs in reionization and in high-redshift galaxy formation.

  7. Differentiation of Microbial Species and Strains in Coculture Biofilms by Multivariate Analysis of Laser Desorption Postionization Mass Spectra

    SciTech Connect

    University of Illinois at Chicago; Montana State University; Bhardwaj, Chhavi; Cui, Yang; Hofstetter, Theresa; Liu, Suet Yi; Bernstein, Hans C.; Carlson, Ross P.; Ahmed, Musahid; Hanley, Luke

    2013-04-01

    7.87 to 10.5 eV vacuum ultraviolet (VUV) photon energies were used in laser desorption postionization mass spectrometry (LDPI-MS) to analyze biofilms comprised of binary cultures of interacting microorganisms. The effect of photon energy was examined using both tunable synchrotron and laser sources of VUV radiation. Principal components analysis (PCA) was applied to the MS data to differentiate species in Escherichia coli-Saccharomyces cerevisiae coculture biofilms. PCA of LDPI-MS also differentiated individual E. coli strains in a biofilm comprised of two interacting gene deletion strains, even though these strains differed from the wild type K-12 strain by no more than four gene deletions each out of approximately 2000 genes. PCA treatment of 7.87 eV LDPI-MS data separated the E. coli strains into three distinct groups two ?pure? groups and a mixed region. Furthermore, the ?pure? regions of the E. coli cocultures showed greater variance by PCA when analyzed by 7.87 eV photon energies than by 10.5 eV radiation. Comparison of the 7.87 and 10.5 eV data is consistent with the expectation that the lower photon energy selects a subset of low ionization energy analytes while 10.5 eV is more inclusive, detecting a wider range of analytes. These two VUV photon energies therefore give different spreads via PCA and their respective use in LDPI-MS constitute an additional experimental parameter to differentiate strains and species.

  8. Effects of ammonium bicarbonate on the electrospray mass spectra of proteins: evidence for bubble-induced unfolding.

    PubMed

    Hedges, Jason B; Vahidi, Siavash; Yue, Xuanfeng; Konermann, Lars

    2013-07-01

    Many protein investigations by electrospray ionization (ESI) mass spectrometry (MS) strive to ensure a "native" solvent environment, i.e., nondenaturing conditions up to the point of gas-phase ion formation. Ideally, these studies would employ a volatile pH buffer to mitigate changes in H(+) concentration that can occur during ESI. Ammonium acetate is a commonly used additive, despite its low buffering capacity at pH 7. Ammonium bicarbonate provides greatly improved pH stabilization, thus offering an interesting alternative. Surprisingly, protein analyses in bicarbonate at pH 7 tend to result in the formation of very high charge states, similar to those obtained when electrospraying unfolded proteins in a denaturing solvent. This effect has been reported previously (Sterling, H. J.; Cassou, C. A.; Susa, A. C.; Williams, E. R. Anal. Chem. 2012, 84, 3795), but its exact mechanistic origin remains unclear. ESI-mediated unfolding does not take place in acetate under otherwise identical conditions. We demonstrate that heating of protein-containing bicarbonate solutions results in extensive foaming, caused by CO2 outgassing. In contrast, acetate solutions do not generate foam. Protein denaturation caused by gas bubbles is a well-known phenomenon. Adsorption to the gas/liquid interface is accompanied by major conformational changes that allow the protein to act as a surfactant. The foaming of beer is a manifestation of this effect. Bubble formation in bicarbonate during ESI is facilitated by collisional and blackbody droplet heating. Our data imply that heat and bubbles act synergistically to cause unfolding during the electrospray process, while proteins reside in ESI droplets. Because of this effect we advise against the use of ammonium bicarbonate for native ESI-MS. Ammonium acetate represents a gentler droplet environment, despite its low buffering capacity.

  9. Simultaneous thermogravimetric modulated beam mass spectrometry and time-of-flight velocity spectra measurements of thermal decomposition products from HMX and RDX

    SciTech Connect

    Behrens, R. Jr.

    1987-01-01

    Simultaneous thermogravimetric modulated beam mass spectrometry (STMBMS) and time-of-flight (TOF) velocity spectra measurements of the time-dependent thermal decomposition products from HMX and RDX show two primary reaction channels. One is a condensed phase autocatalytic reaction that produces N/sub 2/O, H/sub 2/CO, 1-nitoso-3,5,7-trinitro-1,3,5,7-tetrazacyclooctane, and a hydrocarbon-like nonvolatile residue (NVR) as its final products. The other is a gas phase reaction that produces NO/sub 2/, H/sub 2/O, NO and hydroxy-s-triazine as its final products. The catalyst in the condensed phase reaction is probably formaldehyde, the NVR, or both. The gas phase channel appears to be a chain reaction that may be initiated by the abstraction of a hydrogen atom from a CH/sub 2/ group. Under the conditions of these experiments, the HMX decomposes only through the condensed phase channel and the RDX decomposes through both channels. To assure that only thermal decomposition products are measured with the mass spectrometer, the ion fragmentation of HMX was measured as a function of electron energy. Ion fragmentation of HMX was observed down to 12.4 eV indicating that appearance potential measurements do not eliminate ion signals from ion fragmentation of the HMX reactant.

  10. X-Ray Spectra of the High-mass X-Ray Binary 4U 1700-37 Using BeppoSAX, Suzaku, and RXTE Observations

    NASA Astrophysics Data System (ADS)

    Seifina, Elena; Titarchuk, Lev; Shaposhnikov, Nikolai

    2016-04-01

    We present an X-ray spectral analysis of the high-mass binary 4U 1700-37 during its hard-soft state evolution. We use BeppoSAX, Suzaku, and Rossi X-ray Timing Explorer observations for this investigation. We argue that the X-ray broadband spectra during all of the spectral states can be adequately reproduced by a model consisting of a low-temperature blackbody component, two Comptonized components which are both due to the presence of a Compton cloud (CC) that up-scatters seed photons of Ts1 ≲ 1.4 keV and Ts2 < 1 keV, and an iron-line component. Using this model, we find that the photon power-law index is almost constant, Γ1 ∼ 2 for all spectral states. However, Γ2 shows behavior that is dependent on the spectral state. Namely, Γ2 is quasi-constant at the level of Γ2 ∼ 2 while the CC plasma temperature {{kT}}e(2) is less than 40 keV; on the other hand, Γ2 is in the range of 1.3 < Γ2 < 2 when {{kT}}e(2) is greater than 40 keV. We explain this quasi-stability of Γ during most of the hard-soft transitions of 4U 1700-37 in the framework of a model in which the resulting spectrum is described by two Comptonized components. We find that these Comptonized spectral components of the high-mass X-ray binaries 4U 1700-37 are similar to those previously found in neutron star (NS) sources. This index dependence versus both the mass accretion rate and kTe revealed in 4U 1700-37 is universal observational evidence for the presence of an NS in 4U 1700-37.

  11. Mass

    SciTech Connect

    Quigg, Chris

    2007-12-05

    In the classical physics we inherited from Isaac Newton, mass does not arise, it simply is. The mass of a classical object is the sum of the masses of its parts. Albert Einstein showed that the mass of a body is a measure of its energy content, inviting us to consider the origins of mass. The protons we accelerate at Fermilab are prime examples of Einsteinian matter: nearly all of their mass arises from stored energy. Missing mass led to the discovery of the noble gases, and a new form of missing mass leads us to the notion of dark matter. Starting with a brief guided tour of the meanings of mass, the colloquium will explore the multiple origins of mass. We will see how far we have come toward understanding mass, and survey the issues that guide our research today.

  12. Search for physics beyond the standard model in dilepton mass spectra in proton-proton collisions at √s = 8 TeV

    DOE PAGES

    Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Fabjan, C.; Friedl, M.; Frühwirth, R.; et al

    2015-04-07

    Dimuon and dielectron mass spectra, obtained from data resulting from proton-proton collisions at 8 TeV and recorded by the CMS experiment, are used to search for both narrow resonances and broad deviations from standard model predictions. The data correspond to an integrated luminosity of 20.6 (19.7) fb–1 for the dimuon (dielectron) channel. No evidence for non-standard-model physics is observed and 95% confidence level limits are set on parameters from a number of new physics models. The narrow resonance analyses exclude a Sequential Standard Model Z SSM ' resonance lighter than 2.90 TeV, a superstring-inspired Z ψ ' lighter than 2.57more » TeV, and Randall-Sundrum Kaluza-Klein gravitons with masses below 2.73, 2.35, and 1.27 TeV for couplings of 0.10, 0.05, and 0.01, respectively. A notable feature is that the limits have been calculated in a model-independent way to enable straightforward reinterpretation in any model predicting a resonance structure. The observed events are also interpreted within the framework of two non-resonant analyses: one based on a large extra dimensions model and one based on a quark and lepton compositeness model with a left-left isoscalar contact interaction. Lower limits are established on MS, the scale characterizing the onset of quantum gravity, which range from 4.9 to 3.3 TeV, where the number of additional spatial dimensions varies from 3 to 7. Thus lower limits on Λ, the energy scale parameter for the contact interaction, are found to be 12.0 (15.2) TeV for destructive (constructive) interference in the dimuon channel and 13.5 (18.3) TeV in the dielectron channel.« less

  13. Search for physics beyond the standard model in dilepton mass spectra in proton-proton collisions at √s = 8 TeV

    SciTech Connect

    Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Fabjan, C.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Knünz, V.; Krammer, M.; Krätschmer, I.; Liko, D.; Mikulec, I.; Rabady, D.; Rahbaran, B.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Taurok, A.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C. -E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Bansal, M.; Bansal, S.; Cornelis, T.; De Wolf, E. A.; Janssen, X.; Knutsson, A.; Luyckx, S.; Ochesanu, S.; Rougny, R.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Blekman, F.; Blyweert, S.; D’Hondt, J.; Daci, N.; Heracleous, N.; Keaveney, J.; Lowette, S.; Maes, M.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Villella, I.; Caillol, C.; Clerbaux, B.; De Lentdecker, G.; Dobur, D.; Favart, L.; Gay, A. P. R.; Grebenyuk, A.; Léonard, A.; Mohammadi, A.; Perniè, L.; Reis, T.; Seva, T.; Thomas, L.; Vander Velde, C.; Vanlaer, P.; Wang, J.; Zenoni, F.; Adler, V.; Beernaert, K.; Benucci, L.; Cimmino, A.; Costantini, S.; Crucy, S.; Dildick, S.; Fagot, A.; Garcia, G.; Mccartin, J.; Ocampo Rios, A. A.; Ryckbosch, D.; Salva Diblen, S.; Sigamani, M.; Strobbe, N.; Thyssen, F.; Tytgat, M.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bruno, G.; Castello, R.; Caudron, A.; Ceard, L.; Da Silveira, G. G.; Delaere, C.; du Pree, T.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Jafari, A.; Jez, P.; Komm, M.; Lemaitre, V.; Nuttens, C.; Pagano, D.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Vizan Garcia, J. M.; Beliy, N.; Caebergs, T.; Daubie, E.; Hammad, G. H.; Aldá Júnior, W. L.; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Dos Reis Martins, T.; Mora Herrera, C.; Pol, M. E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Malbouisson, H.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santaolalla, J.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Bernardes, C. A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Aleksandrov, A.; Genchev, V.; Iaydjiev, P.; Marinov, A.; Piperov, S.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Hadjiiska, R.; Kozhuharov, V.; Litov, L.; Pavlov, B.; Petkov, P.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Du, R.; Jiang, C. H.; Plestina, R.; Romeo, F.; Tao, J.; Wang, Z.; Asawatangtrakuldee, C.; Ban, Y.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Zou, W.; Avila, C.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; Gomez Moreno, B.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Polic, D.; Puljak, I.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Kadija, K.; Luetic, J.; Mekterovic, D.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Bodlak, M.; Finger, M.; Finger, M.; Assran, Y.; Elgammal, S.; Mahmoud, M. A.; Radi, A.; Kadastik, M.; Murumaa, M.; Raidal, M.; Tiko, A.; Eerola, P.; Fedi, G.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Kortelainen, M. J.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Baffioni, S.; Beaudette, F.; Busson, P.; Charlot, C.; Dahms, T.; Dalchenko, M.; Dobrzynski, L.; Filipovic, N.; Florent, A.; Granier de Cassagnac, R.; Mastrolorenzo, L.; Miné, P.; Mironov, C.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Paganini, P.; Regnard, S.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Veelken, C.; Yilmaz, Y.; Zabi, A.; Agram, J. -L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J. -M.; Chabert, E. C.; Collard, C.; Conte, E.; Fontaine, J. -C.; Gelé, D.; Goerlach, U.; Goetzmann, C.; Le Bihan, A. -C.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Beaupere, N.; Boudoul, G.; Bouvier, E.; Brochet, S.; Carrillo Montoya, C. A.; Chasserat, J.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fan, J.; Fay, J.; Gascon, S.; Gouzevitch, M.; Ille, B.; Kurca, T.; Lethuillier, M.; Mirabito, L.; Perries, S.; Ruiz Alvarez, J. D.; Sabes, D.; Sgandurra, L.; Sordini, V.; Vander Donckt, M.; Verdier, P.; Viret, S.; Xiao, H.; Tsamalaidze, Z.; Autermann, C.; Beranek, S.; Bontenackels, M.; Edelhoff, M.; Feld, L.; Hindrichs, O.; Klein, K.; Ostapchuk, A.; Perieanu, A.; Raupach, F.; Sammet, J.; Schael, S.; Weber, H.; Wittmer, B.; Zhukov, V.; Ata, M.; Brodski, M.; Dietz-Laursonn, E.; Duchardt, D.; Erdmann, M.; Fischer, R.; Güth, A.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Klingebiel, D.; Knutzen, S.; Kreuzer, P.; Merschmeyer, M.; Meyer, A.; Millet, P.; Olschewski, M.; Padeken, K.; Papacz, P.; Pook, T.; Reithler, H.; Schmitz, S. A.; Sonnenschein, L.; Teyssier, D.; Thüer, S.; Weber, M.; Cherepanov, V.; Erdogan, Y.; Flügge, G.; Geenen, H.; Geisler, M.; Haj Ahmad, W.; Heister, A.; Hoehle, F.; Kargoll, B.; Kress, T.; Kuessel, Y.; Künsken, A.; Lingemann, J.; Nowack, A.; Nugent, I. M.; Perchalla, L.; Pooth, O.; Stahl, A.; Asin, I.; Bartosik, N.; Behr, J.; Behrenhoff, W.; Behrens, U.; Bell, A. J.; Bergholz, M.; Bethani, A.; Borras, K.; Burgmeier, A.; Cakir, A.; Calligaris, L.; Campbell, A.; Choudhury, S.; Costanza, F.; Diez Pardos, C.; Dooling, S.; Dorland, T.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Flucke, G.; Garay Garcia, J.; Geiser, A.; Gunnellini, P.; Hauk, J.; Hempel, M.; Horton, D.; Jung, H.; Kalogeropoulos, A.; Kasemann, M.; Katsas, P.; Kieseler, J.; Kleinwort, C.; Krücker, D.; Lange, W.; Leonard, J.; Lipka, K.; Lobanov, A.; Lohmann, W.; Lutz, B.; Mankel, R.; Marfin, I.; Melzer-Pellmann, I. -A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Naumann-Emme, S.; Nayak, A.; Novgorodova, O.; Ntomari, E.; Perrey, H.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Ribeiro Cipriano, P. M.; Roland, B.; Ron, E.; Sahin, M. Ö.; Salfeld-Nebgen, J.; Saxena, P.; Schmidt, R.; Schoerner-Sadenius, T.; Schröder, M.; Seitz, C.; Spannagel, S.; Vargas Trevino, A. D. R.; Walsh, R.; Wissing, C.; Aldaya Martin, M.; Blobel, V.; Centis Vignali, M.; Draeger, A. R.; Erfle, J.; Garutti, E.; Goebel, K.; Görner, M.; Haller, J.; Hoffmann, M.; Höing, R. S.; Kirschenmann, H.; Klanner, R.; Kogler, R.; Lange, J.; Lapsien, T.; Lenz, T.; Marchesini, I.; Ott, J.; Peiffer, T.; Pietsch, N.; Poehlsen, J.; Poehlsen, T.; Rathjens, D.; Sander, C.; Schettler, H.; Schleper, P.; Schlieckau, E.; Schmidt, A.; Seidel, M.; Sola, V.; Stadie, H.; Steinbrück, G.; Troendle, D.; Usai, E.; Vanelderen, L.; Vanhoefer, A.; Barth, C.; Baus, C.; Berger, J.; Böser, C.; Butz, E.; Chwalek, T.; De Boer, W.; Descroix, A.; Dierlamm, A.; Feindt, M.; Frensch, F.; Giffels, M.; Hartmann, F.; Hauth, T.; Husemann, U.; Katkov, I.; Kornmayer, A.; Kuznetsova, E.; Lobelle Pardo, P.; Mozer, M. U.; Müller, Th.; Nürnberg, A.; Quast, G.; Rabbertz, K.; Ratnikov, F.; Röcker, S.; Simonis, H. J.; Stober, F. M.; Ulrich, R.; Wagner-Kuhr, J.; Wayand, S.; Weiler, T.; Wolf, R.; Anagnostou, G.; Daskalakis, G.; Geralis, T.; Giakoumopoulou, V. A.; Kyriakis, A.; Loukas, D.; Markou, A.; Markou, C.; Psallidas, A.; Topsis-Giotis, I.; Agapitos, A.; Kesisoglou, S.; Panagiotou, A.; Saoulidou, N.; Stiliaris, E.; Aslanoglou, X.; Evangelou, I.; Flouris, G.; Foudas, C.; Kokkas, P.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Bencze, G.; Hajdu, C.; Hidas, P.; Horvath, D.; Sikler, F.; Veszpremi, V.; Vesztergombi, G.; Zsigmond, A. J.; Beni, N.; Czellar, S.; Karancsi, J.; Molnar, J.; Palinkas, J.; Szillasi, Z.; Raics, P.; Trocsanyi, Z. L.; Ujvari, B.; Swain, S. K.; Beri, S. B.; Bhatnagar, V.; Gupta, R.; Bhawandeep, U.; Kalsi, A. K.; Kaur, M.; Kumar, R.; Mittal, M.; Nishu, N.; Singh, J. B.; Kumar, Ashok; Kumar, Arun; Ahuja, S.; Bhardwaj, A.; Choudhary, B. C.; Kumar, A.; Malhotra, S.; Naimuddin, M.; Ranjan, K.; Sharma, V.; Banerjee, S.; Bhattacharya, S.; Chatterjee, K.; Dutta, S.; Gomber, B.; Jain, Sa.; Jain, Sh.; Khurana, R.; Modak, A.; Mukherjee, S.; Roy, D.; Sarkar, S.; Sharan, M.; Abdulsalam, A.; Dutta, D.; Kailas, S.; Kumar, V.; Mohanty, A. K.; Pant, L. M.; Shukla, P.; Topkar, A.; Aziz, T.; Banerjee, S.; Bhowmik, S.; Chatterjee, R. M.; Dewanjee, R. K.; Dugad, S.; Ganguly, S.; Ghosh, S.; Guchait, M.; Gurtu, A.; Kole, G.; Kumar, S.; Maity, M.; Majumder, G.; Mazumdar, K.; Mohanty, G. B.; Parida, B.; Sudhakar, K.; Wickramage, N.; Bakhshiansohi, H.; Behnamian, H.; Etesami, S. M.; Fahim, A.; Goldouzian, R.; Khakzad, M.; Mohammadi Najafabadi, M.; Naseri, M.; Paktinat Mehdiabadi, S.; Rezaei Hosseinabadi, F.; Safarzadeh, B.; Zeinali, M.; Felcini, M.; Grunewald, M.; Abbrescia, M.; Barbone, L.; Calabria, C.; Chhibra, S. S.; Colaleo, A.; Creanza, D.; De Filippis, N.; De Palma, M.; Fiore, L.; Iaselli, G.; Maggi, G.; Maggi, M.; My, S.; Nuzzo, S.; Pompili, A.; Pugliese, G.; Radogna, R.; Selvaggi, G.; Sharma, A.; Silvestris, L.; Venditti, R.; Zito, G.; Abbiendi, G.; Benvenuti, A. C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Brigliadori, L.; Campanini, R.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Codispoti, G.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Primavera, F.; Rossi, A. M.; Rovelli, T.; Siroli, G. P.; Tosi, N.; Travaglini, R.; Albergo, S.; Cappello, G.; Chiorboli, M.; Costa, S.; Giordano, F.; Potenza, R.; Tricomi, A.; Tuve, C.; Barbagli, G.; Ciulli, V.; Civinini, C.; D’Alessandro, R.; Focardi, E.; Gallo, E.; Gonzi, S.; Gori, V.; Lenzi, P.; Meschini, M.; Paoletti, S.; Sguazzoni, G.; Tropiano, A.; Benussi, L.; Bianco, S.; Fabbri, F.; Piccolo, D.; Ferretti, R.; Ferro, F.; Lo Vetere, M.; Robutti, E.; Tosi, S.; Dinardo, M. E.; Fiorendi, S.; Gennai, S.; Gerosa, R.; Ghezzi, A.; Govoni, P.; Lucchini, M. T.; Malvezzi, S.; Manzoni, R. A.; Martelli, A.; Marzocchi, B.; Menasce, D.; Moroni, L.; Paganoni, M.; Pedrini, D.; Ragazzi, S.; Redaelli, N.; Tabarelli de Fatis, T.; Buontempo, S.; Cavallo, N.; Di Guida, S.; Fabozzi, F.; Iorio, A. O. M.; Lista, L.; Meola, S.; Merola, M.; Paolucci, P.; Azzi, P.; Bacchetta, N.; Bisello, D.; Branca, A.; Carlin, R.; Checchia, P.; Dall’Osso, M.; Dorigo, T.; Dosselli, U.; Galanti, M.; Gasparini, F.; Gasparini, U.; Giubilato, P.; Gozzelino, A.; Kanishchev, K.; Lacaprara, S.; Margoni, M.; Meneguzzo, A. T.; Pazzini, J.; Pozzobon, N.; Ronchese, P.; Simonetto, F.; Torassa, E.; Tosi, M.; Zotto, P.; Zucchetta, A.; Zumerle, G.; Gabusi, M.; Ratti, S. P.; Re, V.; Riccardi, C.; Salvini, P.; Vitulo, P.; Biasini, M.; Bilei, G. M.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Mantovani, G.; Menichelli, M.; Saha, A.; Santocchia, A.; Spiezia, A.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Broccolo, G.; Castaldi, R.; Ciocci, M. A.; Dell’Orso, R.; Donato, S.; Fiori, F.; Foà, L.; Giassi, A.; Grippo, M. T.; Ligabue, F.; Lomtadze, T.; Martini, L.; Messineo, A.; Moon, C. S.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Serban, A. T.; Spagnolo, P.; Squillacioti, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Vernieri, C.; Barone, L.; Cavallari, F.; D’imperio, G.; Del Re, D.; Diemoz, M.; Grassi, M.; Jorda, C.; Longo, E.; Margaroli, F.; Meridiani, P.; Micheli, F.; Nourbakhsh, S.; Organtini, G.; Paramatti, R.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Soffi, L.; Traczyk, P.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bellan, R.; Biino, C.; Cartiglia, N.; Casasso, S.; Costa, M.; Degano, A.; Demaria, N.; Finco, L.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Musich, M.; Obertino, M. M.; Ortona, G.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Potenza, A.; Romero, A.; Ruspa, M.; Sacchi, R.; Solano, A.; Staiano, A.; Tamponi, U.; Belforte, S.; Candelise, V.; Casarsa, M.; Cossutti, F.; Della Ricca, G.; Gobbo, B.; La Licata, C.; Marone, M.; Schizzi, A.; Umer, T.; Zanetti, A.; Chang, S.; Kropivnitskaya, A.; Nam, S. K.; Kim, D. H.; Kim, G. N.; Kim, M. S.; Kong, D. J.; Lee, S.; Oh, Y. D.; Park, H.; Sakharov, A.; Son, D. C.; Kim, T. J.; Kim, J. Y.; Song, S.; Choi, S.; Gyun, D.; Hong, B.; Jo, M.; Kim, H.; Kim, Y.; Lee, B.; Lee, K. S.; Park, S. K.; Roh, Y.; Yoo, H. D.; Choi, M.; Kim, J. H.; Park, I. C.; Ryu, G.; Ryu, M. S.; Choi, Y.; Choi, Y. K.; Goh, J.; Kim, D.; Kwon, E.; Lee, J.; Seo, H.; Yu, I.; Juodagalvis, A.; Komaragiri, J. R.; Ali, M. A. B. Md; Castilla-Valdez, H.; De La Cruz-Burelo, E.; Heredia-de La Cruz, I.; Hernandez-Almada, A.; Lopez-Fernandez, R.; Sanchez-Hernandez, A.; Carrillo Moreno, S.; Vazquez Valencia, F.; Pedraza, I.; Salazar Ibarguen, H. A.; Casimiro Linares, E.; Morelos Pineda, A.; Krofcheck, D.; Butler, P. H.; Reucroft, S.; Ahmad, A.; Ahmad, M.; Hassan, Q.; Hoorani, H. R.; Khalid, S.; Khan, W. A.; Khurshid, T.; Shah, M. A.; Shoaib, M.; Bialkowska, H.; Bluj, M.; Boimska, B.; Frueboes, T.; Górski, M.; Kazana, M.; Nawrocki, K.; Romanowska-Rybinska, K.; Szleper, M.; Zalewski, P.; Brona, G.; Bunkowski, K.; Cwiok, M.; Dominik, W.; Doroba, K.; Kalinowski, A.; Konecki, M.; Krolikowski, J.; Misiura, M.; Olszewski, M.; Wolszczak, W.; Bargassa, P.; Beirão Da Cruz E Silva, C.; Faccioli, P.; Ferreira Parracho, P. G.; Gallinaro, M.; Lloret Iglesias, L.; Nguyen, F.; Rodrigues Antunes, J.; Seixas, J.; Varela, J.; Vischia, P.; Golutvin, I.; Gorbunov, I.; Kamenev, A.; Karjavin, V.; Konoplyanikov, V.; Kozlov, G.; Lanev, A.; Malakhov, A.; Matveev, V.; Moisenz, P.; Palichik, V.; Perelygin, V.; Savina, M.; Shmatov, S.; Shulha, S.; Skatchkov, N.; Smirnov, V.; Zarubin, A.; Golovtsov, V.; Ivanov, Y.; Kim, V.; Levchenko, P.; Murzin, V.; Oreshkin, V.; Smirnov, I.; Sulimov, V.; Uvarov, L.; Vavilov, S.; Vorobyev, A.; Vorobyev, An.; Andreev, Yu.; Dermenev, A.; Gninenko, S.; Golubev, N.; Kirsanov, M.; Krasnikov, N.; Pashenkov, A.; Tlisov, D.; Toropin, A.; Epshteyn, V.; Gavrilov, V.; Lychkovskaya, N.; Popov, V.; Safronov, G.; Semenov, S.; Spiridonov, A.; Stolin, V.; Vlasov, E.; Zhokin, A.; Andreev, V.; Azarkin, M.; Dremin, I.; Kirakosyan, M.; Leonidov, A.; Mesyats, G.; Rusakov, S. V.; Vinogradov, A.; Belyaev, A.; Boos, E.; Bunichev, V.; Dubinin, M.; Dudko, L.; Gribushin, A.; Klyukhin, V.; Kodolova, O.; Lokhtin, I.; Obraztsov, S.; Perfilov, M.; Savrin, V.; Snigirev, A.; Azhgirey, I.; Bayshev, I.; Bitioukov, S.; Kachanov, V.; Kalinin, A.; Konstantinov, D.; Krychkine, V.; Petrov, V.; Ryutin, R.; Sobol, A.; Tourtchanovitch, L.; Troshin, S.; Tyurin, N.; Uzunian, A.; Volkov, A.; Adzic, P.; Ekmedzic, M.; Milosevic, J.; Rekovic, V.; Alcaraz Maestre, J.; Battilana, C.; Calvo, E.; Cerrada, M.; Chamizo Llatas, M.; Colino, N.; De La Cruz, B.; Delgado Peris, A.; Domínguez Vázquez, D.; Escalante Del Valle, A.; Fernandez Bedoya, C.; Fernández Ramos, J. P.; Flix, J.; Fouz, M. C.; Garcia-Abia, P.; Gonzalez Lopez, O.; Goy Lopez, S.; Hernandez, J. M.; Josa, M. I.; Navarro De Martino, E.; Pérez-Calero Yzquierdo, A.; Puerta Pelayo, J.; Quintario Olmeda, A.; Redondo, I.; Romero, L.; Soares, M. S.; Albajar, C.; de Trocóniz, J. F.; Missiroli, M.; Moran, D.; Brun, H.; Cuevas, J.; Fernandez Menendez, J.; Folgueras, S.; Gonzalez Caballero, I.; Brochero Cifuentes, J. A.; Cabrillo, I. J.; Calderon, A.; Duarte Campderros, J.; Fernandez, M.; Gomez, G.; Graziano, A.; Lopez Virto, A.; Marco, J.; Marco, R.; Martinez Rivero, C.; Matorras, F.; Munoz Sanchez, F. J.; Piedra Gomez, J.; Rodrigo, T.; Rodríguez-Marrero, A. Y.; Ruiz-Jimeno, A.; Scodellaro, L.; Vila, I.; Vilar Cortabitarte, R.; Abbaneo, D.; Auffray, E.; Auzinger, G.; Bachtis, M.; Baillon, P.; Ball, A. H.; Barney, D.; Benaglia, A.; Bendavid, J.; Benhabib, L.; Benitez, J. F.; Bernet, C.; Bloch, P.; Bocci, A.; Bonato, A.; Bondu, O.; Botta, C.; Breuker, H.; Camporesi, T.; Cerminara, G.; Colafranceschi, S.; D’Alfonso, M.; d’Enterria, D.; Dabrowski, A.; David, A.; De Guio, F.; De Roeck, A.; De Visscher, S.; Di Marco, E.; Dobson, M.; Dordevic, M.; Dorney, B.; Dupont-Sagorin, N.; Elliott-Peisert, A.; Eugster, J.; Franzoni, G.; Funk, W.; Gigi, D.; Gill, K.; Giordano, D.; Girone, M.; Glege, F.; Guida, R.; Gundacker, S.; Guthoff, M.; Hammer, J.; Hansen, M.; Harris, P.; Hegeman, J.; Innocente, V.; Janot, P.; Kousouris, K.; Krajczar, K.; Lecoq, P.; Lourenço, C.; Magini, N.; Malgeri, L.; Mannelli, M.; Marrouche, J.; Masetti, L.; Meijers, F.; Mersi, S.; Meschi, E.; Moortgat, F.; Morovic, S.; Mulders, M.; Musella, P.; Orsini, L.; Pape, L.; Perez, E.; Perrozzi, L.; Petrilli, A.; Petrucciani, G.; Pfeiffer, A.; Pierini, M.; Pimiä, M.; Piparo, D.; Plagge, M.; Racz, A.; Rolandi, G.; Rovere, M.; Sakulin, H.; Schäfer, C.; Schwick, C.; Sharma, A.; Siegrist, P.; Silva, P.; Simon, M.; Sphicas, P.; Spiga, D.; Steggemann, J.; Stieger, B.; Stoye, M.; Takahashi, Y.; Treille, D.; Tsirou, A.; Veres, G. I.; Wardle, N.; Wöhri, H. K.; Wollny, H.; Zeuner, W. D.; Bertl, W.; Deiters, K.; Erdmann, W.; Horisberger, R.; Ingram, Q.; Kaestli, H. C.; Kotlinski, D.; Langenegger, U.; Renker, D.; Rohe, T.; Bachmair, F.; Bäni, L.; Bianchini, L.; Buchmann, M. A.; Casal, B.; Chanon, N.; Dissertori, G.; Dittmar, M.; Donegà, M.; Dünser, M.; Eller, P.; Grab, C.; Hits, D.; Hoss, J.; Lustermann, W.; Mangano, B.; Marini, A. C.; Martinez Ruiz del Arbol, P.; Masciovecchio, M.; Meister, D.; Mohr, N.; Nägeli, C.; Nessi-Tedaldi, F.; Pandolfi, F.; Pauss, F.; Peruzzi, M.; Quittnat, M.; Rebane, L.; Rossini, M.; Starodumov, A.; Takahashi, M.; Theofilatos, K.; Wallny, R.; Weber, H. A.; Amsler, C.; Canelli, M. F.; Chiochia, V.; De Cosa, A.; Hinzmann, A.; Hreus, T.; Kilminster, B.; Lange, C.; Millan Mejias, B.; Ngadiuba, J.; Robmann, P.; Ronga, F. J.; Taroni, S.; Verzetti, M.; Yang, Y.; Cardaci, M.; Chen, K. H.; Ferro, C.; Kuo, C. M.; Lin, W.; Lu, Y. J.; Volpe, R.; Yu, S. S.; Chang, P.; Chang, Y. H.; Chang, Y. W.; Chao, Y.; Chen, K. F.; Chen, P. H.; Dietz, C.; Grundler, U.; Hou, W. -S.; Kao, K. Y.; Lei, Y. J.; Liu, Y. F.; Lu, R. -S.; Majumder, D.; Petrakou, E.; Tzeng, Y. M.; Wilken, R.; Asavapibhop, B.; Singh, G.; Srimanobhas, N.; Suwonjandee, N.; Adiguzel, A.; Bakirci, M. N.; Cerci, S.; Dozen, C.; Dumanoglu, I.; Eskut, E.; Girgis, S.; Gokbulut, G.; Gurpinar, E.; Hos, I.; Kangal, E. E.; Kayis Topaksu, A.; Onengut, G.; Ozdemir, K.; Ozturk, S.; Polatoz, A.; Sunar Cerci, D.; Tali, B.; Topakli, H.; Vergili, M.; Akin, I. V.; Bilin, B.; Bilmis, S.; Gamsizkan, H.; Karapinar, G.; Ocalan, K.; Sekmen, S.; Surat, U. E.; Yalvac, M.; Zeyrek, M.; Gülmez, E.; Isildak, B.; Kaya, M.; Kaya, O.; Cankocak, K.; Vardarlı, F. I.; Levchuk, L.; Sorokin, P.; Brooke, J. J.; Clement, E.; Cussans, D.; Flacher, H.; Goldstein, J.; Grimes, M.; Heath, G. P.; Heath, H. F.; Jacob, J.; Kreczko, L.; Lucas, C.; Meng, Z.; Newbold, D. M.; Paramesvaran, S.; Poll, A.; Senkin, S.; Smith, V. J.; Williams, T.; Bell, K. W.; Belyaev, A.; Brew, C.; Brown, R. M.; Cockerill, D. J. A.; Coughlan, J. A.; Harder, K.; Harper, S.; Olaiya, E.; Petyt, D.; Shepherd-Themistocleous, C. H.; Thea, A.; Tomalin, I. R.; Womersley, W. J.; Worm, S. D.; Baber, M.; Bainbridge, R.; Buchmuller, O.; Burton, D.; Colling, D.; Cripps, N.; Cutajar, M.; Dauncey, P.; Davies, G.; Della Negra, M.; Dunne, P.; Ferguson, W.; Fulcher, J.; Futyan, D.; Gilbert, A.; Hall, G.; Iles, G.; Jarvis, M.; Karapostoli, G.; Kenzie, M.; Lane, R.; Lucas, R.; Lyons, L.; Magnan, A. -M.; Malik, S.; Mathias, B.; Nash, J.; Nikitenko, A.; Pela, J.; Pesaresi, M.; Petridis, K.; Raymond, D. M.; Rogerson, S.; Rose, A.; Seez, C.; Sharp, P.; Tapper, A.; Vazquez Acosta, M.; Virdee, T.; Zenz, S. C.; Cole, J. E.; Hobson, P. R.; Khan, A.; Kyberd, P.; Leggat, D.; Leslie, D.; Martin, W.; Reid, I. D.; Symonds, P.; Teodorescu, L.; Turner, M.; Dittmann, J.; Hatakeyama, K.; Kasmi, A.; Liu, H.; Scarborough, T.; Charaf, O.; Cooper, S. I.; Henderson, C.; Rumerio, P.; Avetisyan, A.; Bose, T.; Fantasia, C.; Lawson, P.; Richardson, C.; Rohlf, J.; John, J. St.; Sulak, L.; Alimena, J.; Berry, E.; Bhattacharya, S.; Christopher, G.; Cutts, D.; Demiragli, Z.; Dhingra, N.; Ferapontov, A.; Garabedian, A.; Heintz, U.; Kukartsev, G.; Laird, E.; Landsberg, G.; Luk, M.; Narain, M.; Segala, M.; Sinthuprasith, T.; Speer, T.; Swanson, J.; Breedon, R.; Breto, G.; Calderon De La Barca Sanchez, M.; Chauhan, S.; Chertok, M.; Conway, J.; Conway, R.; Cox, P. T.; Erbacher, R.; Gardner, M.; Ko, W.; Lander, R.; Miceli, T.; Mulhearn, M.; Pellett, D.; Pilot, J.; Ricci-Tam, F.; Searle, M.; Shalhout, S.; Smith, J.; Squires, M.; Stolp, D.; Tripathi, M.; Wilbur, S.; Yohay, R.; Cousins, R.; Everaerts, P.; Farrell, C.; Hauser, J.; Ignatenko, M.; Rakness, G.; Takasugi, E.; Valuev, V.; Weber, M.; Burt, K.; Clare, R.; Ellison, J.; Gary, J. W.; Hanson, G.; Heilman, J.; Ivova Rikova, M.; Jandir, P.; Kennedy, E.; Lacroix, F.; Long, O. R.; Luthra, A.; Malberti, M.; Nguyen, H.; Olmedo Negrete, M.; Shrinivas, A.; Sumowidagdo, S.; Wimpenny, S.; Andrews, W.; Branson, J. G.; Cerati, G. B.; Cittolin, S.; D’Agnolo, R. T.; Evans, D.; Holzner, A.; Kelley, R.; Klein, D.; Lebourgeois, M.; Letts, J.; Macneill, I.; Olivito, D.; Padhi, S.; Palmer, C.; Pieri, M.; Sani, M.; Sharma, V.; Simon, S.; Sudano, E.; Tadel, M.; Tu, Y.; Vartak, A.; Welke, C.; Würthwein, F.; Yagil, A.; Barge, D.; Bradmiller-Feld, J.; Campagnari, C.; Danielson, T.; Dishaw, A.; Dutta, V.; Flowers, K.; Franco Sevilla, M.; Geffert, P.; George, C.; Golf, F.; Gouskos, L.; Incandela, J.; Justus, C.; Mccoll, N.; Richman, J.; Stuart, D.; To, W.; West, C.; Yoo, J.; Apresyan, A.; Bornheim, A.; Bunn, J.; Chen, Y.; Duarte, J.; Mott, A.; Newman, H. B.; Pena, C.; Rogan, C.; Spiropulu, M.; Timciuc, V.; Vlimant, J. R.; Wilkinson, R.; Xie, S.; Zhu, R. Y.; Azzolini, V.; Calamba, A.; Carlson, B.; Ferguson, T.; Iiyama, Y.; Paulini, M.; Russ, J.; Vogel, H.; Vorobiev, I.; Cumalat, J. P.; Ford, W. T.; Gaz, A.; Luiggi Lopez, E.; Nauenberg, U.; Smith, J. G.; Stenson, K.; Ulmer, K. A.; Wagner, S. R.; Alexander, J.; Chatterjee, A.; Chu, J.; Dittmer, S.; Eggert, N.; Mirman, N.; Nicolas Kaufman, G.; Patterson, J. R.; Ryd, A.; Salvati, E.; Skinnari, L.; Sun, W.; Teo, W. D.; Thom, J.; Thompson, J.; Tucker, J.; Weng, Y.; Winstrom, L.; Wittich, P.; Winn, D.; Abdullin, S.; Albrow, M.; Anderson, J.; Apollinari, G.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Bolla, G.; Burkett, K.; Butler, J. N.; Cheung, H. W. K.; Chlebana, F.; Cihangir, S.; Elvira, V. D.; Fisk, I.; Freeman, J.; Gao, Y.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Hanlon, J.; Hare, D.; Harris, R. M.; Hirschauer, J.; Hooberman, B.; Jindariani, S.; Johnson, M.; Joshi, U.; Kaadze, K.; Klima, B.; Kreis, B.; Kwan, S.; Linacre, J.; Lincoln, D.; Lipton, R.; Liu, T.; Lykken, J.; Maeshima, K.; Marraffino, J. M.; Martinez Outschoorn, V. I.; Maruyama, S.; Mason, D.; McBride, P.; Merkel, P.; Mishra, K.; Mrenna, S.; Musienko, Y.; Nahn, S.; Newman-Holmes, C.; O’Dell, V.; Prokofyev, O.; Sexton-Kennedy, E.; Sharma, S.; Soha, A.; Spalding, W. J.; Spiegel, L.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vidal, R.; Whitbeck, A.; Whitmore, J.; Yang, F.; Acosta, D.; Avery, P.; Bortignon, P.; Bourilkov, D.; Carver, M.; Cheng, T.; Curry, D.; Das, S.; De Gruttola, M.; Di Giovanni, G. P.; Field, R. D.; Fisher, M.; Furic, I. K.; Hugon, J.; Konigsberg, J.; Korytov, A.; Kypreos, T.; Low, J. F.; Matchev, K.; Milenovic, P.; Mitselmakher, G.; Muniz, L.; Rinkevicius, A.; Shchutska, L.; Snowball, M.; Sperka, D.; Yelton, J.; Zakaria, M.; Hewamanage, S.; Linn, S.; Markowitz, P.; Martinez, G.; Rodriguez, J. L.; Adams, T.; Askew, A.; Bochenek, J.; Diamond, B.; Haas, J.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Prosper, H.; Veeraraghavan, V.; Weinberg, M.; Baarmand, M. M.; Hohlmann, M.; Kalakhety, H.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Bazterra, V. E.; Berry, D.; Betts, R. R.; Bucinskaite, I.; Cavanaugh, R.; Evdokimov, O.; Gauthier, L.; Gerber, C. E.; Hofman, D. J.; Khalatyan, S.; Kurt, P.; Moon, D. H.; O’Brien, C.; Silkworth, C.; Turner, P.; Varelas, N.; Albayrak, E. A.; Bilki, B.; Clarida, W.; Dilsiz, K.; Duru, F.; Haytmyradov, M.; Merlo, J. -P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Rahmat, R.; Sen, S.; Tan, P.; Tiras, E.; Wetzel, J.; Yetkin, T.; Yi, K.; Barnett, B. A.; Blumenfeld, B.; Bolognesi, S.; Fehling, D.; Gritsan, A. V.; Maksimovic, P.; Martin, C.; Swartz, M.; Baringer, P.; Bean, A.; Benelli, G.; Bruner, C.; Kenny, R. P.; Malek, M.; Murray, M.; Noonan, D.; Sanders, S.; Sekaric, J.; Stringer, R.; Wang, Q.; Wood, J. S.; Chakaberia, I.; Ivanov, A.; Khalil, S.; Makouski, M.; Maravin, Y.; Saini, L. K.; Shrestha, S.; Skhirtladze, N.; Svintradze, I.; Gronberg, J.; Lange, D.; Rebassoo, F.; Wright, D.; Baden, A.; Belloni, A.; Calvert, B.; Eno, S. C.; Gomez, J. A.; Hadley, N. J.; Kellogg, R. G.; Kolberg, T.; Lu, Y.; Marionneau, M.; Mignerey, A. C.; Pedro, K.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Apyan, A.; Barbieri, R.; Bauer, G.; Busza, W.; Cali, I. A.; Chan, M.; Di Matteo, L.; Gomez Ceballos, G.; Goncharov, M.; Gulhan, D.; Klute, M.; Lai, Y. S.; Lee, Y. -J.; Levin, A.; Luckey, P. D.; Ma, T.; Paus, C.; Ralph, D.; Roland, C.; Roland, G.; Stephans, G. S. F.; Stöckli, F.; Sumorok, K.; Velicanu, D.; Veverka, J.; Wyslouch, B.; Yang, M.; Zanetti, M.; Zhukova, V.; Dahmes, B.; Gude, A.; Kao, S. C.; Klapoetke, K.; Kubota, Y.; Mans, J.; Pastika, N.; Rusack, R.; Singovsky, A.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bloom, K.; Bose, S.; Claes, D. R.; Dominguez, A.; Gonzalez Suarez, R.; Keller, J.; Knowlton, D.; Kravchenko, I.; Lazo-Flores, J.; Malik, S.; Meier, F.; Snow, G. R.; Zvada, M.; Dolen, J.; Godshalk, A.; Iashvili, I.; Kharchilava, A.; Kumar, A.; Rappoccio, S.; Alverson, G.; Barberis, E.; Baumgartel, D.; Chasco, M.; Haley, J.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; Trocino, D.; Wang, R. -J.; Wood, D.; Zhang, J.; Hahn, K. A.; Kubik, A.; Mucia, N.; Odell, N.; Pollack, B.; Pozdnyakov, A.; Schmitt, M.; Stoynev, S.; Sung, K.; Velasco, M.; Won, S.; Brinkerhoff, A.; Chan, K. M.; Drozdetskiy, A.; Hildreth, M.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Luo, W.; Lynch, S.; Marinelli, N.; Pearson, T.; Planer, M.; Ruchti, R.; Valls, N.; Wayne, M.; Wolf, M.; Woodard, A.; Antonelli, L.; Brinson, J.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Hart, A.; Hill, C.; Hughes, R.; Kotov, K.; Ling, T. Y.; Puigh, D.; Rodenburg, M.; Smith, G.; Winer, B. L.; Wolfe, H.; Wulsin, H. W.; Driga, O.; Elmer, P.; Hebda, P.; Hunt, A.; Koay, S. A.; Lujan, P.; Marlow, D.; Medvedeva, T.; Mooney, M.; Olsen, J.; Piroué, P.; Quan, X.; Saka, H.; Stickland, D.; Tully, C.; Werner, J. S.; Zuranski, A.; Brownson, E.; Mendez, H.; Ramirez Vargas, J. E.; Barnes, V. E.; Benedetti, D.; Bortoletto, D.; De Mattia, M.; Gutay, L.; Hu, Z.; Jha, M. K.; Jones, M.; Jung, K.; Kress, M.; Leonardo, N.; Lopes Pegna, D.; Maroussov, V.; Miller, D. H.; Neumeister, N.; Radburn-Smith, B. C.; Shi, X.; Shipsey, I.; Silvers, D.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Zablocki, J.; Zheng, Y.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Ecklund, K. M.; Geurts, F. J. M.; Li, W.; Michlin, B.; Padley, B. P.; Redjimi, R.; Roberts, J.; Zabel, J.; Betchart, B.; Bodek, A.; Covarelli, R.; de Barbaro, P.; Demina, R.; Eshaq, Y.; Ferbel, T.; Garcia-Bellido, A.; Goldenzweig, P.; Han, J.; Harel, A.; Khukhunaishvili, A.; Petrillo, G.; Vishnevskiy, D.; Ciesielski, R.; Demortier, L.; Goulianos, K.; Lungu, G.; Mesropian, C.; Arora, S.; Barker, A.; Chou, J. P.; Contreras-Campana, C.; Contreras-Campana, E.; Duggan, D.; Ferencek, D.; Gershtein, Y.; Gray, R.; Halkiadakis, E.; Hidas, D.; Kaplan, S.; Lath, A.; Panwalkar, S.; Park, M.; Patel, R.; Salur, S.; Schnetzer, S.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Rose, K.; Spanier, S.; York, A.; Bouhali, O.; Castaneda Hernandez, A.; Eusebi, R.; Flanagan, W.; Gilmore, J.; Kamon, T.; Khotilovich, V.; Krutelyov, V.; Montalvo, R.; Osipenkov, I.; Pakhotin, Y.; Perloff, A.; Roe, J.; Rose, A.; Safonov, A.; Sakuma, T.; Suarez, I.; Tatarinov, A.; Akchurin, N.; Cowden, C.; Damgov, J.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Kovitanggoon, K.; Kunori, S.; Lee, S. W.; Libeiro, T.; Volobouev, I.; Appelt, E.; Delannoy, A. G.; Greene, S.; Gurrola, A.; Johns, W.; Maguire, C.; Mao, Y.; Melo, A.; Sharma, M.; Sheldon, P.; Snook, B.; Tuo, S.; Velkovska, J.; Arenton, M. W.; Boutle, S.; Cox, B.; Francis, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Lin, C.; Neu, C.; Wood, J.; Clarke, C.; Harr, R.; Karchin, P. E.; Kottachchi Kankanamge Don, C.; Lamichhane, P.; Sturdy, J.; Belknap, D. A.; Carlsmith, D.; Cepeda, M.; Dasu, S.; Dodd, L.; Duric, S.; Friis, E.; Hall-Wilton, R.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Lazaridis, C.; Levine, A.; Loveless, R.; Mohapatra, A.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ross, I.; Sarangi, T.; Savin, A.; Smith, W. H.; Taylor, D.; Verwilligen, P.; Vuosalo, C.; Woods, N.

    2015-04-07

    Dimuon and dielectron mass spectra, obtained from data resulting from proton-proton collisions at 8 TeV and recorded by the CMS experiment, are used to search for both narrow resonances and broad deviations from standard model predictions. The data correspond to an integrated luminosity of 20.6 (19.7) fb–1 for the dimuon (dielectron) channel. No evidence for non-standard-model physics is observed and 95% confidence level limits are set on parameters from a number of new physics models. The narrow resonance analyses exclude a Sequential Standard Model Z SSM ' resonance lighter than 2.90 TeV, a superstring-inspired Z ψ ' lighter than 2.57 TeV, and Randall-Sundrum Kaluza-Klein gravitons with masses below 2.73, 2.35, and 1.27 TeV for couplings of 0.10, 0.05, and 0.01, respectively. A notable feature is that the limits have been calculated in a model-independent way to enable straightforward reinterpretation in any model predicting a resonance structure. The observed events are also interpreted within the framework of two non-resonant analyses: one based on a large extra dimensions model and one based on a quark and lepton compositeness model with a left-left isoscalar contact interaction. Lower limits are established on MS, the scale characterizing the onset of quantum gravity, which range from 4.9 to 3.3 TeV, where the number of additional spatial dimensions varies from 3 to 7. Thus lower limits on Λ, the energy scale parameter for the contact interaction, are found to be 12.0 (15.2) TeV for destructive (constructive) interference in the dimuon channel and 13.5 (18.3) TeV in the dielectron channel.

  14. Comparing Multiple Reaction Monitoring and Sequential Window Acquisition of All Theoretical Mass Spectra for the Relative Quantification of Barley Gluten in Selectively Bred Barley Lines.

    PubMed

    Colgrave, Michelle L; Byrne, Keren; Blundell, Malcolm; Heidelberger, Sibylle; Lane, Catherine S; Tanner, Gregory J; Howitt, Crispin A

    2016-09-20

    Celiac disease (CD) is a disease of the small intestine that occurs in genetically susceptible subjects triggered by the ingestion of cereal gluten proteins for which the only treatment is strict adherence to a life-long gluten-free diet. Barley contains four gluten protein families, and the existence of barley genotypes that do not accumulate the B-, C-, and D-hordeins paved the way for the development of an ultralow gluten phenotype. Using conventional breeding strategies, three null mutations behaving as recessive alleles were combined to create a hordein triple-null barley variety. Proteomics has become an invaluable tool for characterization and quantification of the protein complement of cereal grains. In this study multiple reaction monitoring (MRM) mass spectrometry, viewed as the gold standard for peptide quantification, was compared to the data-independent acquisition strategy known as SWATH-MS (sequential window acquisition of all theoretical mass spectra). SWATH-MS was comparable (p < 0.001) to MRM-MS for 32/33 peptides assessed across the four families of hordeins (gluten) in eight barley lines. The results of SWATH-MS analysis further confirmed the absence of the B-, C-, and D-hordeins in the triple-null barley line and showed significantly reduced levels ranging from <1% to 16% relative to wild-type (WT) cv Sloop for the minor γ-hordein class. SWATH-MS represents a valuable tool for quantitative proteomics based on its ability to generate reproducible data comparable with MRM-MS, but has the added benefits of allowing reinterrogation of data to improve analytical performance, ask new questions, and in this case perform quantification of trypsin-resistant proteins (C-hordeins) through analysis of their semi- or nontryptic fragments. PMID:27533879

  15. Analysis on heavy quarkonia transitions with pion emission in terms of the QCD multipole expansion and determination of mass spectra of hybrids

    SciTech Connect

    Ke, Hong-Wei; Tang, Jian; Hao, Xi-Qing; Li, Xue-Qian

    2007-10-01

    One of the most important tasks in high energy physics is the search for the exotic states, such as glueball, hybrid, and multiquark states. The transitions {psi}(ns){yields}{psi}(ms)+{pi}{pi} and {upsilon}(ns){yields}{upsilon}(ms)+{pi}{pi} attract great attention because they may reveal characteristics of hybrids. In this work, we analyze those transition modes in terms of the theoretical framework established by Yan and Kuang. It is interesting to notice that the intermediate states between the two gluon emissions are hybrids, therefore by fitting the data, we are able to determine the mass spectra of hybrids. The ground hybrid states are predicted as 4.23 GeV (for charmonium) and 10.79 GeV (for bottonium) which do not correspond to any states measured in recent experiments, thus it may imply that, very possibly, hybrids mix with regular quarkonia to constitute physical states. Comprehensive comparisons of the potentials for hybrids whose parameters are obtained in this scenario with the lattice results are presented.

  16. A Simple Approach for Obtaining High Resolution, High Sensitivity ¹H NMR Metabolite Spectra of Biofluids with Limited Mass Supply

    SciTech Connect

    Hu, Jian Zhi; Rommereim, Donald N.; Wind, Robert A.; Minard, Kevin R.; Sears, Jesse A.

    2006-11-01

    A simple approach is reported that yields high resolution, high sensitivity ¹H NMR spectra of biofluids with limited mass supply. This is achieved by spinning a capillary sample tube containing a biofluid at the magic angle at a frequency of about 80Hz. A 2D pulse sequence called ¹H PASS is then used to produce a high-resolution ¹H NMR spectrum that is free from magnetic susceptibility induced line broadening. With this new approach a high resolution ¹H NMR spectrum of biofluids with a volume less than 1.0 µl can be easily achieved at a magnetic field strength as low as 7.05T. Furthermore, the methodology facilitates easy sample handling, i.e., the samples can be directly collected into inexpensive and disposable capillary tubes at the site of collection and subsequently used for NMR measurements. In addition, slow magic angle spinning improves magnetic field shimming and is especially suitable for high throughput investigations. In this paper first results are shown obtained in a magnetic field of 7.05T on urine samples collected from mice using a modified commercial NMR probe.

  17. Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectra of poly(butylene adipate).

    PubMed

    Rizzarelli, Paola; Puglisi, Concetto; Montaudo, Giorgio

    2006-01-01

    Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS/MS) was employed to analyze four poly(butylene adipate) (PBAd) oligomers and to investigate their fragmentation pathways as a continuation of our work on the MALDI-TOF/TOF-MS/MS study of synthetic polymers. MALDI-TOF/TOF-MS/MS analysis was performed on oligomers terminated by carboxyl and hydroxyl groups, methyl adipate and hydroxyl groups, dihydroxyl groups, and dicarboxyl groups. The sodium adducts of these oligomers were selected as precursor ions. Different end groups do not influence the fragmentation of sodiated polyester oligomers and similar series of product ions were observed in all the MALDI-TOF/TOF-MS/MS spectra. According to the structures of the most abundant product ions identified in the present work, three fragmentation pathways have been proposed to occur most frequently in PBAd: beta-hydrogen-transfer rearrangement, leading to the selective cleavage of the --O--CH(2)-- bonds; --CH(2)--CH(2)-- (beta--beta) bond cleavage in the adipate moiety; and ester bond scission.

  18. An Automated, Low Mass, Low Power Drill for Acquiring Subsurface Samples of Ground Ice for Astrobiology Studies on Earth and on Mars

    NASA Technical Reports Server (NTRS)

    Briggs, G. A.; McKay, C.; George, J.; Derkowski, G.; Cooper, G.; Zacny, K.; Baker, R. Fincher; Pollard, W.; Clifford, S.

    2003-01-01

    As a project that is part of NASA s Astrobiology Technology & Instrument Development Program (ASTID), we are developing a low mass (approx.20kg) drill that will be operated without drilling fluids and at very low power levels (approx.60 watts electrical) to access and retrieve samples from permafrost regions of Earth and Mars. The drill, designed and built as a joint effort by NASA JSC and Baker-Hughes International, takes the form of a down-hole unit attached to a cable so that it can, in principle, be scaled easily to reach significant depths. A parallel laboratory effort is being carried out at UC Berkeley to characterize the physics of dry drilling under martian conditions of pressure, temperature and atmospheric composition. Data from the UCB and JSC laboratory experiments are being used as input to a drill simulation program which is under development to provide autonomous control of the drill. The first Arctic field test of the unit is planned for May 2004. A field expedition to Eureka on Ellesmere Island in Spring 2003 provided an introduction for several team members to the practical aspects of drilling under Arctic conditions. The field effort was organized by Wayne Pollard of McGill University and Christopher McKay of NASA ARC. A conventional science drill provided by New Zealand colleagues was used to recover ground ice cores for analysis of their microbial content and also to develop techniques using tracers to track the depth of penetration of contamination from the core surface into the interior of the samples.

  19. Correlating mass physical properties with ALOS reflectance spectra for intertidal sediments from the Ba Lat Estuary (northern Vietnam): an exploratory laboratory study

    NASA Astrophysics Data System (ADS)

    Ngoc, Nguyen Thi; Koike, Katsuaki; Tue, Nguyen Tai

    2013-08-01

    Characterization of the sediment composition of tidal flats and monitoring of their spatiotemporal changes has become an important part of the sustainable management of coastal environments. To accurately classify sediments through remote sensing, a comprehensive understanding of sediment reflectance spectra is indispensable. The present laboratory-based study explores the performance of the high spatial resolution (10 × 10 m) Advanced Land Observing Satellite (ALOS) launched in 2006. Relationships between reflectance spectra (bands 1 to 4) and four typical mass physical properties were investigated under wet and dry experimental conditions for intertidal sediments sampled near the Ba Lat Estuary in northern Vietnam. Reflectance in the near-infrared region corresponding to ALOS band 4 (0.76-0.89 μm) was found (1) to have a strong negative correlation with sand content (dry wt%) under both wet and dry conditions (linear correlation coefficient r = -0.7859 and -0.8094, respectively), (2) to increase with decreasing relative water content (%) in a given sediment type (r = -0.7748 to -0.9367 for mud, sandy mud, muddy sand, and sand), (3) to have a positive correlation with organic matter content (r = 0.7610 and 0.6460 under wet and dry conditions for contents >0.20 dry wt%), and (4) to be insignificantly correlated with mineral composition assessed in terms of contents (wt%) of quartz, clay minerals, and mica group minerals. Positive relationships between reflectance and water content for the pooled data of all sediment types (r = 0.6395) or organic matter content contrast with previous findings, and can be attributed to close interrelationships between these properties and the predominance of sand content as controlling factor of reflectance. This study clarifies that ALOS band 4 provides the most useful imagery for intertidal monitoring because its reflectance, as simulated using the laboratory data, shows the strongest correlation with sand content. In a next step

  20. Method for the Compound Annotation of Conjugates in Nontargeted Metabolomics Using Accurate Mass Spectrometry, Multistage Product Ion Spectra and Compound Database Searching.

    PubMed

    Ogura, Tairo; Bamba, Takeshi; Tai, Akihiro; Fukusaki, Eiichiro

    2015-01-01

    Owing to biotransformation, xenobiotics are often found in conjugated form in biological samples such as urine and plasma. Liquid chromatography coupled with accurate mass spectrometry with multistage collision-induced dissociation provides spectral information concerning these metabolites in complex materials. Unfortunately, compound databases typically do not contain a sufficient number of records for such conjugates. We report here on the development of a novel protocol, referred to as ChemProphet, to annotate compounds, including conjugates, using compound databases such as PubChem and ChemSpider. The annotation of conjugates involves three steps: 1. Recognition of the type and number of conjugates in the sample; 2. Compound search and annotation of the deconjugated form; and 3. In silico evaluation of the candidate conjugate. ChemProphet assigns a spectrum to each candidate by automatically exploring the substructures corresponding to the observed product ion spectrum. When finished, it annotates the candidates assigning a rank for each candidate based on the calculated score that ranks its relative likelihood. We assessed our protocol by annotating a benchmark dataset by including the product ion spectra for 102 compounds, annotating the commercially available standard for quercetin 3-glucuronide, and by conducting a model experiment using urine from mice that had been administered a green tea extract. The results show that by using the ChemProphet approach, it is possible to annotate not only the deconjugated molecules but also the conjugated molecules using an automatic interpretation method based on deconjugation that involves multistage collision-induced dissociation and in silico calculated conjugation.

  1. Rock Outcrop Spectra

    NASA Technical Reports Server (NTRS)

    2004-01-01

    The color image on the lower left shows a rock outcrop at Meridiani Planum, Mars. This image was taken by the panoramic camera on the Mars Exploration Rover Opportunity, looking north, and was acquired on the 4th sol, or martian day, of the rover's mission (Jan. 27, 2004). The yellow box outlines an area detailed in the top left image, which is a monochrome (single filter) image from the rover's panoramic camera. The top image uses solid colors to show several regions on or near the rock outcrop from which spectra were extracted: the dark soil above the outcrop (yellow), the distant horizon surface (aqua), a bright rock in the outcrop (green), a darker rock in the outcrop (red), and a small dark cobblestone (blue). Spectra from these regions are shown in the plot to the right.

  2. Acquired color vision deficiency.

    PubMed

    Simunovic, Matthew P

    2016-01-01

    Acquired color vision deficiency occurs as the result of ocular, neurologic, or systemic disease. A wide array of conditions may affect color vision, ranging from diseases of the ocular media through to pathology of the visual cortex. Traditionally, acquired color vision deficiency is considered a separate entity from congenital color vision deficiency, although emerging clinical and molecular genetic data would suggest a degree of overlap. We review the pathophysiology of acquired color vision deficiency, the data on its prevalence, theories for the preponderance of acquired S-mechanism (or tritan) deficiency, and discuss tests of color vision. We also briefly review the types of color vision deficiencies encountered in ocular disease, with an emphasis placed on larger or more detailed clinical investigations.

  3. Hospital-acquired pneumonia

    MedlinePlus

    ... tends to be more serious than other lung infections because: People in the hospital are often very sick and cannot fight off ... prevent pneumonia. Most hospitals have programs to prevent hospital-acquired infections.

  4. Acquired Cerebral Trauma: Epilogue.

    ERIC Educational Resources Information Center

    Bigler, Erin D., Ed.

    1988-01-01

    The article summarizes a series of articles concerning acquired cerebral trauma. Reviewed are technological advances, treatment, assessment, potential innovative therapies, long-term outcome, family impact of chronic brain injury, and prevention. (DB)

  5. [Acquired haemophilia (acquired factor VIII inhibitor)].

    PubMed

    Ceresetto, José M; Duboscq, Cristina; Fondevila, Carlos; Tezanos Pinto, Miguel

    2015-01-01

    Acquired haemophilia is a rare disorder. The clinical picture ranges from mild ecchymosis and anaemia to life threatening bleeding in up to 20% of patients. The disease is produced by an antibody against Factor VIII and it usually occurs in the elderly, with no previous history of a bleeding disorder. It can be associated to an underlying condition such as cancer, autoimmune disorders, drugs or pregnancy. It has a typical laboratory pattern with isolated prolonged activated partial thromboplastin time (aPTT) that fails to correct upon mixing tests with normal plasma and low levels of factor VIII. Treatment recommendations are based on controlling the acute bleeding episodes with either bypassing agent, recombinant activated factor VII or activated prothrombin complex concentrate, and eradication of the antibody with immunosuppressive therapy.

  6. (abstract) Spectra of Comet Hale-Bopp

    NASA Technical Reports Server (NTRS)

    Hanner, M. S.; Hayward, T. L.; Lynch, D. K.; Russell, R. W.

    1996-01-01

    The spectra of Hale-Bopp were acquired in mid-1996 at R > 3.5 AU. Strong silicate emission is present in all the spectra. The shape of the feature is very similar to that seen in comet P/Halley. This is the first time that a strong silicate feature has been detected in a comet beyond 2 AU.

  7. Community-acquired pneumonia.

    PubMed

    Falguera, M; Ramírez, M F

    2015-11-01

    This article not only reviews the essential aspects of community-acquired pneumonia for daily clinical practice, but also highlights the controversial issues and provides the newest available information. Community-acquired pneumonia is considered in a broad sense, without excluding certain variants that, in recent years, a number of authors have managed to delineate, such as healthcare-associated pneumonia. The latter form is nothing more than the same disease that affects more frail patients, with a greater number of risk factors, both sharing an overall common approach. PMID:26186969

  8. Acquired hypofibrinogenemia: current perspectives

    PubMed Central

    Besser, Martin W; MacDonald, Stephen G

    2016-01-01

    Acquired hypofibrinogenemia is most frequently caused by hemodilution and consumption of clotting factors. The aggressive replacement of fibrinogen has become one of the core principles of modern management of massive hemorrhage. The best method for determining the patient’s fibrinogen level remains controversial, and particularly in acquired dysfibrinogenemia, could have major therapeutic implications depending on which quantification method is chosen. This review introduces the available laboratory and point-of-care methods and discusses the relative advantages and limitations. It also discusses current strategies for the correction of hypofibrinogenemia. PMID:27713652

  9. Community-acquired pneumonia.

    PubMed

    Falguera, M; Ramírez, M F

    2015-11-01

    This article not only reviews the essential aspects of community-acquired pneumonia for daily clinical practice, but also highlights the controversial issues and provides the newest available information. Community-acquired pneumonia is considered in a broad sense, without excluding certain variants that, in recent years, a number of authors have managed to delineate, such as healthcare-associated pneumonia. The latter form is nothing more than the same disease that affects more frail patients, with a greater number of risk factors, both sharing an overall common approach.

  10. Acquired Brain Injury Program.

    ERIC Educational Resources Information Center

    Schwartz, Stacey Hunter

    This paper reviews the Acquired Brain Injury (ABI) Program at Coastline Community College (California). The ABI Program is a two-year, for-credit educational curriculum designed to provide structured cognitive retraining for adults who have sustained an ABI due to traumatic (such as motor vehicle accident or fall) or non-traumatic(such as…

  11. Mass loss

    NASA Technical Reports Server (NTRS)

    Goldberg, Leo

    1987-01-01

    Observational evidence for mass loss from cool stars is reviewed. Spectra line profiles are used for the derivation of mass-loss rates with the aid of the equation of continuity. This equation implies steady mass loss with spherical symmetry. Data from binary stars, Mira variables, and red giants in globular clusters are examined. Silicate emission is discussed as a useful indicator of mass loss in the middle infrared spectra. The use of thermal millimeter-wave radiation, Very Large Array (VLA) measurement of radio emission, and OH/IR masers are discussed as a tool for mass loss measurement. Evidence for nonsteady mass loss is also reviewed.

  12. A REVISED CALIBRATION OF THE VIRIAL MASS ESTIMATOR FOR BLACK HOLES IN ACTIVE GALAXIES BASED ON SINGLE-EPOCH Hβ SPECTRA

    SciTech Connect

    Ho, Luis C.; Kim, Minjin

    2015-08-20

    The masses of supermassive black holes (BHs) in broad-line active galactic nuclei (AGNs) can be measured through reverberation mapping, but this method currently cannot be applied to very large samples or to high-redshift AGNs. As a practical alternative, one can devise empirical scaling relations, based on the correlation between broad-line region size and AGN luminosity and the relation between BH mass and bulge stellar velocity dispersion, to estimate the virial masses of BHs from single-epoch spectroscopy. We present a revised calibration of the BH mass estimator for the commonly used Hβ emission line. Our new calibration takes into account the recent determination of the virial coefficient for pseudo and classical bulges.

  13. Community-acquired pneumonia.

    PubMed

    Prina, Elena; Ranzani, Otavio T; Torres, Antoni

    2015-09-12

    Community-acquired pneumonia causes great mortality and morbidity and high costs worldwide. Empirical selection of antibiotic treatment is the cornerstone of management of patients with pneumonia. To reduce the misuse of antibiotics, antibiotic resistance, and side-effects, an empirical, effective, and individualised antibiotic treatment is needed. Follow-up after the start of antibiotic treatment is also important, and management should include early shifts to oral antibiotics, stewardship according to the microbiological results, and short-duration antibiotic treatment that accounts for the clinical stability criteria. New approaches for fast clinical (lung ultrasound) and microbiological (molecular biology) diagnoses are promising. Community-acquired pneumonia is associated with early and late mortality and increased rates of cardiovascular events. Studies are needed that focus on the long-term management of pneumonia.

  14. Systemic Acquired Resistance

    PubMed Central

    2006-01-01

    Upon infection with necrotizing pathogens many plants develop an enhanced resistance to further pathogen attack also in the uninoculated organs. This type of enhanced resistance is referred to as systemic acquired resistance (SAR). In the SAR state, plants are primed (sensitized) to more quickly and more effectively activate defense responses the second time they encounter pathogen attack. Since SAR depends on the ability to access past experience, acquired disease resistance is a paradigm for the existence of a form of “plant memory”. Although the phenomenon has been known since the beginning of the 20th century, major progress in the understanding of SAR was made over the past sixteen years. This review covers the current knowledge of molecular, biochemical and physiological mechanisms that are associated with SAR. PMID:19521483

  15. DETERMINATION OF ION AND NEUTRAL LOSS COMPOSITIONS AND DECONVOLUTION OF PRODUCT ION MASS SPECTRA USING AN ORTHOGONAL ACCELERATION, TIME-OF-FLIGHT MASS SPECTROMETER AND AN ION CORRELATION PROGRAM

    EPA Science Inventory

    Exact masses of monoisotopic ions and the relative isotopic abundances (RIAs) of ions greater in mass by 1 and 2 Da than the monoisotopic ion are independent and complementary physical properties useful for istinguishing among ion compositions possible for a given nominal mass. U...

  16. Acquired methemoglobinemia revisited.

    PubMed

    Trapp, Larry; Will, John

    2010-10-01

    Dentistry has two medications in its pain management armamentarium that may cause the potentially life-threatening disorder methemoglobinemia. The first medications are the topical local anesthetics benzocaine and prilocaine. The second medication is the injectable local anesthetic prilocaine. Acquired methemoglobinemia remains a source of morbidity and mortality in dental and medical patients despite the fact that it is better understood now than it was even a decade ago. It is in the interest of all dental patients that their treating dentists review this disorder. The safety of dental patients mandates professional awareness.

  17. Ion Mobility Mass Spectrometry for Extracting Spectra of N-Glycans Directly from Incubation Mixtures Following Glycan Release: Application to Glycans from Engineered Glycoforms of Intact, Folded HIV gp120

    NASA Astrophysics Data System (ADS)

    Harvey, David J.; Sobott, Frank; Crispin, Max; Wrobel, Antoni; Bonomelli, Camille; Vasiljevic, Snezana; Scanlan, Christopher N.; Scarff, Charlotte A.; Thalassinos, Konstantinos; Scrivens, James H.

    2011-03-01

    The analysis of glycosylation from native biological sources is often frustrated by the low abundances of available material. Here, ion mobility combined with electrospray ionization mass spectrometry have been used to extract the spectra of N-glycans released with PNGase F from a serial titration of recombinantly expressed envelope glycoprotein, gp120, from the human immunodeficiency virus (HIV). Analysis was also performed on gp120 expressed in the α-mannosidase inhibitor, and in a matched mammalian cell line deficient in GlcNAc transferase I. Without ion mobility separation, ESI spectra frequently contained no observable ions from the glycans whereas ions from other compounds such as detergents and residual buffer salts were abundant. After ion mobility separation on a Waters T-wave ion mobility mass spectrometer, the N-glycans fell into a unique region of the ion mobility/ m/z plot allowing their profiles to be extracted with good signal:noise ratios. This method allowed N-glycan profiles to be extracted from crude incubation mixtures with no clean-up even in the presence of surfactants such as NP40. Furthermore, this technique allowed clear profiles to be obtained from sub-microgram amounts of glycoprotein. Glycan profiles were similar to those generated by MALDI-TOF MS although they were more susceptible to double charging and fragmentation. Structural analysis could be accomplished by MS/MS experiments in either positive or negative ion mode but negative ion mode gave the most informative spectra and provided a reliable approach to the analysis of glycans from small amounts of glycoprotein.

  18. Storm Spectra

    NASA Technical Reports Server (NTRS)

    2007-01-01

    portion is defined by the day/night boundary (known as the terminator).

    These two images illustrate only a small fraction of the information contained in a single LEISA scan, highlighting just one aspect of the power of infrared spectra for atmospheric studies.

  19. NASA Fuse Cycle 1 Program A100. FUV Spectra of Evolved Late-K and M Stars: Mass Loss revisited and Stellar Activity

    NASA Technical Reports Server (NTRS)

    Harper, Graham M.

    2002-01-01

    Program A100 was awarded 50 ksec of FUSE observing time. Targets alpha TrA (K3 II) and gamma Cru (N13 III) were originally assigned 25 ksec each, to be observed in the medium aperture. Once the in-flight performance and telescope alignment problems were known, the observations were reprogrammed to optimized the scientific return of the program. alpha TrA was scheduled for 25 ksec observations in both the medium and large apertures. The principle aim of this program was to measure the stellar FUV line and continuum emission, in order to estimate the photoionization radiation field and to determine the level of stellar activity through the fluxes in the collisionally excited high temperature diagnostics: C III 977A and O VI 1032,1038A doublet. The medium aperture observations were obtained successfully while the large aperture observations were thought by Johns Hopkins University (JHU)to be lost to satellite problems. There was insufficient signal-to noise in the medium aperture short wavelength SiC channels to do quantitative science. The long wavelength LiF spectra are of high signal-to-noise (SN) and show pronounced emission lines near lambdalambda1100 - 1140A. Emission had been observed at these wavelength in low resolution and low SN ORFEUS-SPAS 11 spectra obtained by Dupree & Brickhouse (1998 ApJ 500, L33), however, they were unable to identify these features. One of the first problems faced in the early FUSE mission was establishing a reliable wavelength scale, especially between the different channels. With the medium aperture data in hand we decided to identify the features and thereby establish an absolute wavelength scale for the channels where the emission occurred. We first established that the emission was fluorescent. and then we constructed a fluorescent line formation model for all neutrals. and singly ionized species with atomic numbers up to 28, and the H2 molecule. We used datasets of radiative rates and energy levels which were as complete as

  20. Community-acquired pneumonia.

    PubMed

    Polverino, E; Torres Marti, A

    2011-02-01

    Despite the remarkable advances in antibiotic therapies, diagnostic tools, prevention campaigns and intensive care, community-acquired pneumonia (CAP) is still among the primary causes of death worldwide, and there have been no significant changes in mortality in the last decades. The clinical and economic burden of CAP makes it a major public health problem, particularly for children and the elderly. This issue provides a clinical overview of CAP, focusing on epidemiology, economic burden, diagnosis, risk stratification, treatment, clinical management, and prevention. Particular attention is given to some aspects related to the clinical management of CAP, such as the microbial etiology and the available tools to achieve it, the usefulness of new and old biomarkers, and antimicrobial and other non-antibiotic adjunctive therapies. Possible scenarios in which pneumonia does not respond to treatment are also analyzed to improve clinical outcomes of CAP. PMID:21242952

  1. An ultra-tolerant database search reveals that a myriad of modified peptides contributes to unassigned spectra in shotgun proteomics

    PubMed Central

    Chick, Joel M.; Kolippakkam, Deepak; Nusinow, David P.; Zhai, Bo; Rad, Ramin; Huttlin, Edward L.; Gygi, Steven P.

    2015-01-01

    Fewer than half of all tandem mass spectrometry (MS/MS) spectra acquired in shotgun proteomics experiments are typically matched to a peptide with high confidence. Here we determine the identity of unassigned peptides using an ultra-tolerant Sequest database search that allows peptide matching even with modifications of unknown masses up to ±500 Da. In a proteome-wide dataset on HEK293 cells (9,513 proteins and 396,736 peptides), this approach matched an additional 184,000 modified peptides, which were linked to biological and chemical modifications representing 523 distinct mass bins, including phosphorylation, glycosylation, and methylation. We localized all unknown modification masses to specific regions within a peptide. Known modifications were assigned to the correct amino acids with frequencies often >90%. We conclude that at least one third of unassigned spectra arise from peptides with substoichiometric modifications. PMID:26076430

  2. Interpretation of the ion mass spectra in the mass range 25-35 obtained in the inner coma of Halley's comet by the HIS-sensor of the Giotto IMS Experiment

    NASA Technical Reports Server (NTRS)

    Geiss, J.; Altwegg, K.; Anders, E.; Balsiger, H.; Ip, W.-H.; Meier, A.; Neugebauer, M.; Rosenbauer, H.; Shelley, E. G.

    1991-01-01

    The IMS-HIS double-focussing mass spectrometer that flew on the Giotto spacecraft covered the mass per charge range from 12 to 56 (AMU/e). By comparing flight data, calibration data, and results of model calculations of the ion population in the inner coma, the absolute mass scale is established, and ions in the mass range 25 to 35 are identified. Ions resulting from protonation of molecules with high proton affinity are relatively abundant, enabling us to estimate relative source strengths for H2CO, CH3OH, HCN, and H2S, providing for the first time a positive in situ measurement of methanol. Also, upper limits for NO and some hydrocarbons are derived.

  3. Mass spectrometry of analytical derivatives. 1. Cyanide cations in the spectra of N- alkyl-N-perfluoroacyl- α-amino acids and their methyl esters.

    PubMed

    Todua, Nino G; Tretyakov, Kirill V; Mikaia, Anzor I

    2015-01-01

    The central mission for the development of the National Institute of Standards and Technology/National Institutes of Health/Environmental Protection Agency Mass Spectral Library is the acquisition of reference gas chromatography-mass spectrometry data for important compounds and their chemical modification products. The addition of reliable reference data of various derivatives of amino acids to The Library, and the study of their behavior under electron ionization conditions may be useful for their identification, structure elucidation and a better understanding of the data obtained when the same derivatives are subjected to other ionization methods. N-Alkyl-N-perfluoroacyl derivatives of amino acids readily produce previously unreported alkylnitrilium cations of composition [HC≡N-alkyl](+). Homologous [HC≡N-aryl](+) cations are typical for corresponding N-aryl analogs. The formation of other ions characteristic for these derivatives involves oxygen rearrangement giving rise to ions [C(n)F(2n+1)-C≡N(+)C(n)H(2n+1)] and [CnF(2n+1)-C≡N(+)-aryl]. The introduction of an N-benzyl substituent in a molecule favors a process producing benzylidene iminium cations. L-Threonine and L-cysteine derivatives exhibit more fragmentation pathways not typical for other α-amino acids; additionally, the N(ω)- amino group in L-lysine directs the dissociation process and provides structural information on the substitution at the amino functions in the molecule.

  4. Mass spectrometry of analytical derivatives. 1. Cyanide cations in the spectra of N-alkyl-N-perfluoroacyl-α-amino acids and their methyl esters

    PubMed Central

    Todua, Nino G.; Tretyakov, Kirill V.; Mikaia, Anzor I.

    2016-01-01

    The central mission for the development of the National Institute of Standards and Technology/National Institutes of Health/Environmental Protection Agency Mass Spectral Library is the acquisition of reference gas chromatography–mass spectrometry data for important compounds and their chemical modification products. The addition of reliable reference data of various derivatives of amino acids to The Library, and the study of their behavior under electron ionization conditions may be useful for their identification, structure elucidation, and a better understanding of the data obtained when the same derivatives are subjected to other ionization methods. N-Alkyl-N-perfluoroacyl derivatives of amino acids readily produce previously unreported alkylnitrilium cations of composition [HC≡N-alkyl]+. Homologous [HC≡N-aryl]+ cations are typical for corresponding N-aryl analogs. The formation of other ions characteristic for these derivatives involves oxygen rearrangement giving rise to ions [CnF2n+1–C≡N+–CnH2n+1] and [CnF2n+1–C≡N+-aryl]. The introduction of an N-benzyl substituent in a molecule favors a process producing benzylidene iminium cations. l-Threonine and l-cysteine derivatives exhibit more fragmentation pathways not typical for other α-amino acids; additionally, the Nω-amino group in l-lysine directs the dissociation process and provides structural information on the substitution at the amino functions in the molecule. PMID:26307698

  5. Profiling and classification of French propolis by combined multivariate data analysis of planar chromatograms and scanning direct analysis in real time mass spectra.

    PubMed

    Chasset, Thibaut; Häbe, Tim T; Ristivojevic, Petar; Morlock, Gertrud E

    2016-09-23

    Quality control of propolis is challenging, as it is a complex natural mixture of compounds, and thus, very difficult to analyze and standardize. Shown on the example of 30 French propolis samples, a strategy for an improved quality control was demonstrated in which high-performance thin-layer chromatography (HPTLC) fingerprints were evaluated in combination with selected mass signals obtained by desorption-based scanning mass spectrometry (MS). The French propolis sample extracts were separated by a newly developed reversed phase (RP)-HPTLC method. The fingerprints obtained by two different detection modes, i.e. after (1) derivatization and fluorescence detection (FLD) at UV 366nm and (2) scanning direct analysis in real time (DART)-MS, were analyzed by multivariate data analysis. Thus, RP-HPTLC-FLD and RP-HPTLC-DART-MS fingerprints were explored and the best classification was obtained using both methods in combination with pattern recognition techniques, such as principal component analysis. All investigated French propolis samples were divided in two types and characteristic patterns were observed. Phenolic compounds such as caffeic acid, p-coumaric acid, chrysin, pinobanksin, pinobanksin-3-acetate, galangin, kaempferol, tectochrysin and pinocembrin were identified as characteristic marker compounds of French propolis samples. This study expanded the research on the European poplar type of propolis and confirmed the presence of two botanically different types of propolis, known as the blue and orange types. PMID:27599799

  6. Discovery of 90 Type Ia supernovae among 700 000 Sloan spectra: the Type Ia supernova rate versus galaxy mass and star formation rate at redshift ˜0.1

    NASA Astrophysics Data System (ADS)

    Graur, Or; Maoz, Dan

    2013-04-01

    Using a method to discover and classify supernovae (SNe) in galaxy spectra, we find 90 Type Ia SNe (SNe Ia) and 10 Type II SNe among the ˜700 000 galaxy spectra in the Sloan Digital Sky Survey Data Release 7 that have star-formation histories (SFHs) derived with the VErsatile SPectral Analysis code (VESPA). We use the SN Ia sample to measure SN Ia rates per unit stellar mass. We confirm, at the median redshift of the sample, z = 0.1, the inverse dependence on galaxy mass of the SN Ia rate per unit mass, previously reported by Li et al. for a local sample. We further confirm, following Kistler et al., that this relation can be explained by the combination of galaxy `downsizing' and a power-law delay-time distribution (DTD; the distribution of times that elapse between a hypothetical burst of star formation and the subsequent SN Ia explosions) with an index of -1, inherent to the double-degenerate progenitor scenario. We use the method of Maoz et al. to recover the DTD by comparing the number of SNe Ia hosted by each galaxy in our sample with the VESPA-derived SFH of the stellar population within the spectral aperture. In this galaxy sample, which is dominated by old and massive galaxies, we recover a `delayed' component to the DTD of 4.5 ± 0.6 (statistical){_{-0.5}^+0.3} (systematic) × 10- 14 SNe M⊙- 1 yr- 1 for delays in the range >2.4 Gyr. The mass-normalized SN Ia rate, averaged over all masses and redshifts in our galaxy sample, is R_{Ia,M}(z=0.1) = 0.10 ± 0.01 (statistical) ± 0.01 (systematic) SNuM, and the volumetric rate is RIa, V(z = 0.1) = 0.247_{-0.026}^{+0.029} (statistical) _{-0.031}^{+0.016} (systematic) × 10- 4 SNe yr- 1 Mpc- 3. This rate is consistent with the rates and rate evolution from other recent SN Ia surveys, which together also indicate a ˜t-1 DTD.

  7. Towards understanding the tandem mass spectra of protonated oligopeptides. 2: The proline effect in collision-induced dissociation of protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp).

    PubMed

    Bleiholder, Christian; Suhai, Sándor; Harrison, Alex G; Paizs, Béla

    2011-06-01

    The product ion spectra of proline-containing peptides are commonly dominated by y(n) ions generated by cleavage at the N-terminal side of proline residues. This proline effect is investigated in the current work by collision-induced dissociation (CID) of protonated Ala-Ala-Xxx-Pro-Ala (Xxx includes Ala, Ser, Leu, Val, Phe, and Trp) in an electrospray/quadrupole/time-of-flight (QqTOF) mass spectrometer and by quantum chemical calculations on protonated Ala-Ala-Ala-Pro-Ala. The CID spectra of all investigated peptides show a dominant y(2) ion (Pro-Ala sequence). Our computational results show that the proline effect mainly arises from the particularly low threshold energy for the amide bond cleavage N-terminal to the proline residue, and from the high proton affinity of the proline-containing C-terminal fragment produced by this cleavage. These theoretical results are qualitatively supported by the experimentally observed y(2)/b(3) abundance ratios for protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp). In the post-cleavage phase of fragmentation the N-terminal oxazolone fragment with the Ala-Ala-Xxx sequence and Pro-Ala compete for the ionizing proton for these peptides. As the proton affinity of the oxazolone fragment increases, the y(2)/b(3) abundance ratio decreases.

  8. Acquired aplastic anemia.

    PubMed

    Keohane, Elaine M

    2004-01-01

    Acquired aplastic anemia (AA) is a disorder characterized by a profound deficit of hematopoietic stem and progenitor cells, bone marrow hypocellularity, and peripheral blood pancytopenia. It primarily affects children, young adults, and those over 60 years of age. The majority of cases are idiopathic; however, idiosyncratic reactions to some drugs, chemicals, and viruses have been implicated in its etiology. An autoimmune T-cell reaction likely causes the stem cell depletion, but the precise mechanism, as well as the eliciting and target antigens, is unknown. Symptoms vary from severe life-threatening cytopenias to moderate or non-severe disease that does not require transfusion support. The peripheral blood typically exhibits pancytopenia, reticulocytopenia, and normocytic or macrocytic erythrocytes. The bone marrow is hypocellular and may exhibit dysplasia of the erythrocyte precursors. First line treatment for severe AA consists of hematopoietic stem cell transplantation in young patients with HLA identical siblings, while immunosuppression therapy is used for older patients and for those of any age who lack a HLA matched donor. Patients with AA have an increased risk of developing paroxysmal nocturnal hemoglobinuria (PNH), myelodysplastic syndrome (MDS), or acute leukemia. Further elucidation of the pathophysiology of this disease will result in a better understanding of the interrelationship among AA, PNH, and MDS, and may lead to novel targeted therapies.

  9. LipidBlast templates as flexible tools for creating new in-silico tandem mass spectral libraries.

    PubMed

    Kind, Tobias; Okazaki, Yozo; Saito, Kazuki; Fiehn, Oliver

    2014-11-18

    Tandem mass spectral libraries (MS/MS) are usually built by acquiring experimentally measured mass spectra from chemical reference compounds. We here show the versatility of in-silico or computer generated tandem mass spectra that are directly obtained from compound structures. We use the freely available LipidBlast development software to generate 15 000 MS/MS spectra of the glucuronosyldiacylglycerol (GlcADG) lipid class, recently discovered for the first time in plants. The generation of such an in-silico MS/MS library for positive and negative ionization mode took 5 h development time, including the validation of the obtained mass spectra. Such libraries allow for high-throughput annotations of previously unknown glycolipids. The publicly available LipidBlast templates are universally applicable for the development of MS/MS libraries for novel lipid classes.

  10. Observation of micelle solution of decyltrimethylammonium bromide by electrospray ionization mass spectrometry.

    PubMed

    Nohara, D; Bitoh, M

    2000-12-01

    A micelle solution of decyltrimethylammonium bromide (DTAB) was analyzed by electrospray ionization mass spectrometry. Finding an appropriate range of a capillary-skimmer potential was a prerequisite for obtaining a satisfactory spectrum. The mean molecular weight of DTAB aggregates, 10,500, was deduced from a series of mass spectra acquired at different capillary-skimmer potentials. The value was comparable with the micelle weight, previously determined by the light-scattering method.

  11. A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

    SciTech Connect

    Pan, Chongle; Park, Byung H; McDonald, W Hayes; Carey, Patricia A; Banfield, Jillian F.; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Samatova, Nagiza F

    2010-01-01

    Background High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms. Results In this study, a new de novo sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily on mass accuracy information of fragment ions. Consensus sequence tags were inferred for 11,422 spectra with an average peptide length of 5.5 residues from a total of 40,297 input spectra acquired in a 24-hour proteomics measurement of Rhodopseudomonas palustris. The accuracy of inferred consensus sequence tags was 84%. According to our comparison, the performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, in terms of the number of de novo sequenced spectra and the sequencing accuracy. Conclusions Here, we improved de novo sequencing performance by developing a new algorithm specifically for high-resolution tandem mass spectral data. The Vonode algorithm is freely available for download at http://compbio.ornl.gov/Vonode.

  12. Quality evaluation of tandem mass spectral libraries.

    PubMed

    Oberacher, Herbert; Weinmann, Wolfgang; Dresen, Sebastian

    2011-06-01

    Tandem mass spectral libraries are gaining more and more importance for the identification of unknowns in different fields of research, including metabolomics, forensics, toxicology, and environmental analysis. Particularly, the recent invention of reliable, robust, and transferable libraries has increased the general acceptance of these tools. Herein, we report on results obtained from thorough evaluation of the match reliabilities of two tandem mass spectral libraries: the MSforID library established by the Oberacher group in Innsbruck and the Weinmann library established by the Weinmann group in Freiburg. Three different experiments were performed: (1) Spectra of the libraries were searched against their corresponding library after excluding either this single compound-specific spectrum or all compound-specific spectra prior to searching; (2) the libraries were searched against each other using either library as reference set or sample set; (3) spectra acquired on different mass spectrometric instruments were matched to both libraries. Almost 13,000 tandem mass spectra were included in this study. The MSforID search algorithm was used for spectral matching. Statistical evaluation of the library search results revealed that principally both libraries enable the sensitive and specific identification of compounds. Due to higher mass accuracy of the QqTOF compared with the QTrap instrument, matches to the MSforID library were more reliable when comparing spectra with both libraries. Furthermore, only the MSforID library was shown to be efficiently transferable to different kinds of tandem mass spectrometers, including "tandem-in-time" instruments; this is due to the coverage of a large range of different collision energy settings-including the very low range-which is an outstanding characteristics of the MSforID library.

  13. 16 CFR 801.2 - Acquiring and acquired persons.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976 COVERAGE RULES § 801.2 Acquiring... each holds half of V's shares. Therefore, A and B each control V (see § 801.1(b)), and V is included...” are acquiring persons. (b) Except as provided in paragraphs (a) and (b) of § 801.12, the...

  14. 16 CFR 801.2 - Acquiring and acquired persons.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976 COVERAGE RULES § 801.2 Acquiring... each holds half of V's shares. Therefore, A and B each control V (see § 801.1(b)), and V is included...” are acquiring persons. (b) Except as provided in paragraphs (a) and (b) of § 801.12, the...

  15. 16 CFR 801.2 - Acquiring and acquired persons.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ...” are acquiring persons. (b) Except as provided in paragraphs (a) and (b) of § 801.12, the person(s.... Examples: 1. Corporation A (the ultimate parent entity included within person “A”) proposes to acquire Y, a... to be carried out by merging Y into X, a wholly-owned subsidiary of A, with X surviving, and...

  16. 16 CFR 801.2 - Acquiring and acquired persons.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ...” are acquiring persons. (b) Except as provided in paragraphs (a) and (b) of § 801.12, the person(s.... Examples: 1. Corporation A (the ultimate parent entity included within person “A”) proposes to acquire Y, a... to be carried out by merging Y into X, a wholly-owned subsidiary of A, with X surviving, and...

  17. Mass determination of megadalton-DNA electrospray ions using charge detection mass spectrometry.

    PubMed

    Schultz, J C; Hack, C A; Benner, W H

    1998-04-01

    Charge detection mass spectrometry (CD-MS) has been used to determine the mass of double-stranded, circular DNA and single-stranded, circular DNA in the range of 2500 to 8000 base pairs (1.5-5.0 MDa). Simultaneous measurement of the charge and velocity of an electrostatically accelerated ion allows a mass determination of the ion, with instrument calibration determined independently of samples. Positive ion mass spectra of electrosprayed commercial DNA samples supplied in tris(hydroxymethyl)ethylenediaminetetraacetic acid buffer, diluted in 50 vol. % acetonitrile, were obtained without cleanup of the sample. A CD mass spectrum constructed from 3000 ion measurements takes 10 min to acquire and yields the DNA molecular mass directly (mass resolution = 6). The data collected represent progress toward a more automatable alternative to sizing of DNA by gel electrophoresis. In addition to the mass spectra, CD-MS generates charge versus mass plots, which provide another means to investigate the creation and fate of large electrospray ions.

  18. Mass determination of megadalton-DNA Electrospray Ions usingCharge Detection Mass Spectrometry

    SciTech Connect

    Schultz, Jocelyn C.; Hack, Christopher; Benner, Henry W.

    1997-10-01

    Charge detection mass spectrometry (CD-MS) has been used to determine the mass of double-stranded, circular DNA and single-stranded, circular DNA in the range of 2500 to 8000 base pairs (1.5-5.0 MDa). Simultaneous measurement of the charge and velocity of an electrostatically accelerated ion allows a mass determination of the ion, with instrument calibration determined independently of samples. Positive ion mass spectra of electrosprayed commercial DNA samples supplied in tris(hydroxymethyl)ethylenediamine tetraacetic acid buffer, diluted in 50 vol. percent acetonitrile, were obtained without cleanup of the sample. ACD mass spectrum constructed from 3000 ion measurements takes 10 min to acquire and yields the DNA molecular mass directly (mass resolution = 6). The data collected represent progress toward a more automatable alternative to sizing of DNA by gel electrophoresis. In addition to the mass spectra, CD-MS generates charge versus mass plots, which provide another means to investigate the creation and fate of large electrospray ions.

  19. Bar Coding MS(2) Spectra for Metabolite Identification.

    PubMed

    Spalding, Jonathan L; Cho, Kevin; Mahieu, Nathaniel G; Nikolskiy, Igor; Llufrio, Elizabeth M; Johnson, Stephen L; Patti, Gary J

    2016-03-01

    Metabolite identifications are most frequently achieved in untargeted metabolomics by matching precursor mass and full, high-resolution MS(2) spectra to metabolite databases and standards. Here we considered an alternative approach for establishing metabolite identifications that does not rely on full, high-resolution MS(2) spectra. First, we select mass-to-charge regions containing the most informative metabolite fragments and designate them as bins. We then translate each metabolite fragmentation pattern into a binary code by assigning 1's to bins containing fragments and 0's to bins without fragments. With 20 bins, this binary-code system is capable of distinguishing 96% of the compounds in the METLIN MS(2) library. A major advantage of the approach is that it extends untargeted metabolomics to low-resolution triple quadrupole (QqQ) instruments, which are typically less expensive and more robust than other types of mass spectrometers. We demonstrate a method of acquiring MS(2) data in which the third quadrupole of a QqQ instrument cycles over 20 wide isolation windows (coinciding with the location and width of our bins) for each precursor mass selected by the first quadrupole. Operating the QqQ instrument in this mode yields diagnostic bar codes for each precursor mass that can be matched to the bar codes of metabolite standards. Furthermore, our data suggest that using low-resolution bar codes enables QqQ instruments to make MS(2)-based identifications in untargeted metabolomics with a specificity and sensitivity that is competitive to high-resolution time-of-flight technologies.

  20. Acquiring and Organizing Curriculum Materials.

    ERIC Educational Resources Information Center

    Lare, Gary A.

    This book addresses two areas of need in a curriculum materials center--where to find curriculum materials for acquisition and how to organize these materials for efficient and effective access once they are acquired. The book is arranged in two parts: "Acquiring and Organizing the Collection" and "Resources." The book brings together many…

  1. [Modeling Soil Spectral Reflectance with Different Mass Moisture Content].

    PubMed

    Sun, Yue-jun; Zheng, Xiao-po; Qin, Qi-ming; Meng, Qing-ye; Gao, Zhong-ling; Ren, Hua-zhong; Wu, Ling; Wang, Jun; Wang, Jian-hua

    2015-08-01

    The spatio-temporal distribution and variation of soil moisture content have a significant impact on soil temperature, heat balance between land and atmosphere and atmospheric circulation. Hence, it is of great significance to monitor the soil moisture content dynamically at a large scale and to acquire its continuous change during a certain period of time. The object of this paper is to explore the relationship between the mass moisture content of soil and soil spectrum. This was accomplished by building a spectral simulation model of soil with different mass moisture content using hyperspectral remote sensing data. The spectra of soil samples of 8 sampling sites in Beijing were obtained using ASD Field Spectrometer. Their mass moisture contents were measured using oven drying method. Spectra of two soil samples under different mass moisture content were used to construct soil spectral simulation model, and the model was validated using spectra of the other six soil samples. The results show that the accuracy of the model is higher when the mass water content of soil is below field capacity. At last, we used the spectra of three sampling points on campus of Peking University to test the model, and the minimum value of root mean square error between simulated and measured spectral reflectance was 0.0058. Therefore the model is expected to perform well in simulating the spectrum reflectance of different types of soil when mass water content below field capacity. PMID:26672301

  2. Thermal Infrared Spectra of Experimentally Shocked Albitite

    NASA Astrophysics Data System (ADS)

    Johnson, J. R.; Horz, F.; Lucey, P.; Christensen, P.

    2002-12-01

    We have acquired thermal infrared (3-40 microns) hemispherical reflectance and emissivity spectra of shocked samples of a fine-grained (1-5 mm) albitite from Szklary, Poland to determine the spectral degradation effects of shocked albite as a function of increasing shock pressures (17-56 GPa). Reflectance data were acquired using a Nicolet 5SXC FTIR spectrometer at the HIGP, University of Hawaii, and emission spectra were acquired using a Nicolet Nexus 670 emission spectrometer at Arizona State University. These data complement similar previous measurements of experimentally shocked anorthosite relevant to interpreting spectra provided by the Thermal Emission Spectrometer (TES) on Mars Global Surveyor. The samples were shocked using the 25-mm barrel gun at Johnson Space Center and provided ~400 mg per sample. Large (2-10 mm) chips of recovered material were separated from the samples and washed to remove clinging fines, and the residual was powdered to provide a consistent grain size (~20 microns). Spectra were obtained of both the chips and the powder samples. Results for the chips show a progressive loss of spectral features and contrast compared to unshocked samples, while results for the powders show a reduction in the depth of the transparency feature located near 855 wavenumbers (11.7 microns) with increasing pressure. The albite structure retains its crystalline state to higher pressures than anorthosites, consistent with previous transmission spectra. Additional visible/near-infrared (0.35-2.50 microns) measurements of the powdered albitite and anorthosite samples also were acquired at the RELAB facility. These spectra show a decrease in albedo and a loss of water bands near 1.4 and 1.9 microns with increasing pressure. The broad feldspar absorption near 1.25 microns was not present in the albitite sample (possibly due to its fine original grain size) but was present in the anorthosite sample, where its band depth decreased with increasing shock pressures.

  3. A combined strategy of mass fragmentation, post-column cobalt complexation and shift in ultraviolet absorption spectra to determine the uridine 5'-diphospho-glucuronosyltransferase metabolism profiling of flavones after oral administration of a flavone mixture in rats.

    PubMed

    Li, Qiang; Wang, Liping; Dai, Peimin; Zeng, Xuejun; Qi, Xiaoxiao; Zhu, Lijun; Yan, Tongmeng; Wang, Ying; Lu, Linlin; Hu, Ming; Wang, Xinchun; Liu, Zhongqiu

    2015-05-22

    The use of dietary flavones is becoming increasingly popular for their prevention of cancers, cardiovascular diseases, and other diseases. Despite many pharmacokinetic studies on flavone mixtures, the position(s) of glucuronidation sites on the flavone skeleton in vivo remain(s) uncertain because of the lack of a convenient method to differentiate the isomers in biological samples. Accordingly, this study aimed to develop a new strategy to identify the position of the mono-O-glucuronide of flavones in vivo and to simultaneously determine the parent agent and its major metabolites responsible for complex pharmacokinetic characteristics. The novel strategy involves accurate mass measurements of flavone glucuronides, their [Co(II) (flavone glucuronide-H) (4,7-diphenyl-1,10-phenanthroline)2](+) complexes generated via the post-column addition of CoBr2 and 4,7-diphenyl-1,10-phenanthroline, and their mass spectrometric fragmentation by UPLC-DAD-Q-TOF and the comparison of retention times with biosynthesized standards of different isomers that were identified by analyzing the shift in UV spectra compared with the spectra of their respective aglycones. We successfully generated a metabolite profiling of flavones in rat plasma after oral administration of a flavone mixture from Dracocephalum moldavica L., which was used here as the model to demonstrate the strategy. Twelve flavone glucuronides, which were glucuronidated derivatives of acacetin, apigenin, luteolin, diosmetin, chrysoeriol and cirsimaritin, were detected and identified. Glucuronidation of the flavone skeleton at the 3'-/7-position was more prevalent, however, luteolin 4'-glucuronide levels exceeded luteolin 7-glucuronide levels. Based on the UDP-glucuronosyltransferase (UGT) metabolism profiling of flavones in rat plasma, six main compounds (tilianin, acacetin 7-glucuronide, apigenin 7-glucuronide, luteolin 3'-glucuronide, acacetin, and apigenin) were selected as pharmacokinetic markers. Pharmacokinetic

  4. Photon spectra from WIMP annihilation

    SciTech Connect

    Cembranos, J. A. R.; Cruz-Dombriz, A. de la; Dobado, A.; Maroto, A. L.; Lineros, R. A.

    2011-04-15

    If the present dark matter in the Universe annihilates into standard model particles, it must contribute to the fluxes of cosmic rays that are detected on the Earth and, in particular, to the observed gamma-ray fluxes. The magnitude of such a contribution depends on the particular dark matter candidate, but certain features of the produced photon spectra may be analyzed in a rather model-independent fashion. In this work we provide the complete photon spectra coming from WIMP annihilation into standard model particle-antiparticle pairs obtained by extensive Monte Carlo simulations. We present results for each individual annihilation channel and provide analytical fitting formulas for the different spectra for a wide range of WIMP masses.

  5. QUALITATIVE INTERPRETATION OF GALAXY SPECTRA

    SciTech Connect

    Sanchez Almeida, J.; Morales-Luis, A. B.; Terlevich, R.; Terlevich, E.; Cid Fernandes, R. E-mail: abml@iac.es E-mail: eterlevi@inaoep.mx

    2012-09-10

    We describe a simple step-by-step guide to qualitative interpretation of galaxy spectra. Rather than an alternative to existing automated tools, it is put forward as an instrument for quick-look analysis and for gaining physical insight when interpreting the outputs provided by automated tools. Though the recipe is for general application, it was developed for understanding the nature of the Automatic Spectroscopic K-means-based (ASK) template spectra. They resulted from the classification of all the galaxy spectra in the Sloan Digital Sky Survey data release 7, thus being a comprehensive representation of the galaxy spectra in the local universe. Using the recipe, we give a description of the properties of the gas and the stars that characterize the ASK classes, from those corresponding to passively evolving galaxies, to H II galaxies undergoing a galaxy-wide starburst. The qualitative analysis is found to be in excellent agreement with quantitative analyses of the same spectra. We compare the mean ages of the stellar populations with those inferred using the code STARLIGHT. We also examine the estimated gas-phase metallicity with the metallicities obtained using electron-temperature-based methods. A number of byproducts follow from the analysis. There is a tight correlation between the age of the stellar population and the metallicity of the gas, which is stronger than the correlations between galaxy mass and stellar age, and galaxy mass and gas metallicity. The galaxy spectra are known to follow a one-dimensional sequence, and we identify the luminosity-weighted mean stellar age as the affine parameter that describes the sequence. All ASK classes happen to have a significant fraction of old stars, although spectrum-wise they are outshined by the youngest populations. Old stars are metal-rich or metal-poor depending on whether they reside in passive galaxies or in star-forming galaxies.

  6. A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

    SciTech Connect

    Pan, Chongle; Park, Byung H; McDonald, W Hayes; Banfield, Jillian F.; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Samatova, Nagiza F

    2010-01-01

    High-resolution tandem mass spectra can now readily be acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. In this study, a new de novo sequencing algorithm, Vonode, has been developed specifically for such high-resolution tandem mass spectra. To fully exploit the high mass accuracy, sparse noise, and low background of these spectra, a unique scoring system is used to evaluate sequence tags based mainly on mass accuracy information of fragment ions. Consensus sequence tags were inferred for 11,422 spectra with an average peptide length of 5.5 residues from a total of 40,297 input spectra acquired in a 24-hour proteomics measurement of Rhodopseudomonas palustris. The accuracy of inferred consensus sequence tags was 84%. The performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, especially in term of the number of de novo sequenced spectra.

  7. Method for calibrating mass spectrometers

    DOEpatents

    Anderson, Gordon A [Benton City, WA; Brands, Michael D [Richland, WA; Bruce, James E [Schwenksville, PA; Pasa-Tolic, Ljiljana [Richland, WA; Smith, Richard D [Richland, WA

    2002-12-24

    A method whereby a mass spectra generated by a mass spectrometer is calibrated by shifting the parameters used by the spectrometer to assign masses to the spectra in a manner which reconciles the signal of ions within the spectra having equal mass but differing charge states, or by reconciling ions having known differences in mass to relative values consistent with those known differences. In this manner, the mass spectrometer is calibrated without the need for standards while allowing the generation of a highly accurate mass spectra by the instrument.

  8. Night Spectra Quest.

    ERIC Educational Resources Information Center

    Jacobs, Stephen

    1995-01-01

    Presents the Night Spectra Quest, a pocket-sized chart that identifies in color the spectra of all the common night lights and has an integrally mounted, holographic diffraction grating to look through. (JRH)

  9. The structure of BPS spectra

    NASA Astrophysics Data System (ADS)

    Longhi, Pietro

    In this thesis we develop and apply novel techniques for analyzing BPS spectra of supersymmetric quantum field theories of class S. By a combination of wall-crossing, spectral networks and quiver methods we explore the BPS spectra of higher rank four-dimensional N = 2 super Yang-Mills, uncovering surprising new phenomena. Focusing on the SU(3) case, we prove the existence of wild BPS spectra in field theory, featuring BPS states of higher spin whose degeneracies grow exponentially with the energy. The occurrence of wild BPS states is surprising because it appears to be in tension with physical expectations on the behavior of the entropy as a function of the energy scale. The solution to this puzzle comes from realizing that the size of wild BPS states grows rapidly with their mass, and carefully analyzing the volume-dependence of the entropy of BPS states. We also find some interesting structures underlying wild BPS spectra, such as a Regge-like relation between the maximal spin of a BPS multiplet and the square of its mass, and the existence of a universal asymptotic distribution of spin-j irreps within a multiplet of given charge. We also extend the spectral networks construction by introducing a refinement in the topological classification of 2d-4d BPS states, and identifying their spin with a topological invariant known as the "writhe of soliton paths". A careful analysis of the 2d-4d wall-crossing behavior of this refined data reveals that it is described by motivic Kontsevich-Soibelman transformations, controlled by the Protected Spin Character, a protected deformation of the BPS index encoding the spin of BPS states. Our construction opens the way for the systematic study of refined BPS spectra in class S theories. We apply it to several examples, including ones featuring wild BPS spectra, where we find an interesting relation between spectral networks and certain functional equations. For class S theories of A 1 type, we derive an alternative technique for

  10. Acquired plate-like osteoma cutis.

    PubMed

    Vashi, Neelam; Chu, Julie; Patel, Rishi

    2011-10-15

    Plate-like osteoma cutis is a rare disorder that has been historically classified as a congenital syndrome. It has a possible relationship to a mutation in the gene (GNAS1) that encodes the α-subunit of the stimulatory G protein, which regulates adenyl cyclase activity. We report a case of extensive plaque-like masses on the scalp and face with no abnormalities in calcium or phosphate metabolism and no preceding inflammatory cutaneous conditions. With less than ten reported cases, to our knowledge, this is one the few cases of acquired plate-like osteoma cutis described in the literature.

  11. Direct Analysis in Real Time (DART) of an Organothiophosphate at Ultrahigh Resolution by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Tandem Mass Spectrometry

    PubMed Central

    Prokai, Laszlo; Stevens, Stanley M.

    2016-01-01

    Direct analysis in real time (DART) is a recently developed ambient ionization technique for mass spectrometry to enable rapid and sensitive analyses with little or no sample preparation. After swab-based field sampling, the organothiophosphate malathion was analyzed using DART-Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Mass resolution was documented to be over 800,000 in full-scan MS mode and over 1,000,000 for an MS/MS product ion produced by collision-induced dissociation of the protonated analyte. Mass measurement accuracy below 1 ppm was obtained for all DART-generated ions that belonged to the test compound in the mass spectra acquired using only external mass calibration. This high mass measurement accuracy, achievable at present only through FTMS, was required for unequivocal identification of the corresponding molecular formulae. PMID:26784186

  12. Direct Analysis in Real Time (DART) of an Organothiophosphate at Ultrahigh Resolution by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Tandem Mass Spectrometry.

    PubMed

    Prokai, Laszlo; Stevens, Stanley M

    2016-01-01

    Direct analysis in real time (DART) is a recently developed ambient ionization technique for mass spectrometry to enable rapid and sensitive analyses with little or no sample preparation. After swab-based field sampling, the organothiophosphate malathion was analyzed using DART-Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Mass resolution was documented to be over 800,000 in full-scan MS mode and over 1,000,000 for an MS/MS product ion produced by collision-induced dissociation of the protonated analyte. Mass measurement accuracy below 1 ppm was obtained for all DART-generated ions that belonged to the test compound in the mass spectra acquired using only external mass calibration. This high mass measurement accuracy, achievable at present only through FTMS, was required for unequivocal identification of the corresponding molecular formulae. PMID:26784186

  13. Correcting peak deformation in Rosetta's ROSINA/DFMS mass spectrometer

    NASA Astrophysics Data System (ADS)

    De Keyser, Johan; Dhooghe, Frederik; Gibbons, Andrew; Altwegg, Kathrin; Balsiger, Hans; Berthelier, Jean-Jacques; Briois, Christelle; Calmonte, Ursina; Cessateur, Gaël; Equeter, Eddy; Fiethe, Björn; Fuselier, Stephen; Gombosi, Tamas; Gunell, Herbert; Hässig, Myrttha; Le Roy, Léna; Maggiolo, Romain; Neefs, Eddy; Rubin, Martin; Sémon, Thierry

    2016-04-01

    The Double Focusing Mass Spectrometer (DFMS), part of the ROSINA instrument package aboard the European Space Agency's Rosetta spacecraft visiting comet 67P/Churyumov-Gerasimenko, experiences minor deformation of the mass peaks in the high resolution spectra acquired for m/Z = 16, 17, and to a lesser extent 18. A numerical deconvolution technique has been developed with a two-fold purpose. A first goal is to verify whether the most likely cause of the issue, a lack of stability of one of the electric potentials in the electrostatic analyser, can indeed be held responsible for it. The second goal is to correct for the deformation, in view of the important species located around these masses, and to allow a standard further treatment of the spectra in the automated DFMS data processing chain.

  14. Mass spectrometry.

    NASA Technical Reports Server (NTRS)

    Burlingame, A. L.; Johanson, G. A.

    1972-01-01

    Review of the current state of mass spectrometry, indicating its unique importance for advanced scientific research. Mass spectrometry applications in computer techniques, gas chromatography, ion cyclotron resonance, molecular fragmentation and ionization, and isotope labeling are covered. Details are given on mass spectrometry applications in bio-organic chemistry and biomedical research. As the subjects of these applications are indicated alkaloids, carbohydrates, lipids, terpenes, quinones, nucleic acid components, peptides, antibiotics, and human and animal metabolisms. Particular attention is given to the mass spectra of organo-inorganic compounds, inorganic mass spectrometry, surface phenomena such as secondary ion and electron emission, and elemental and isotope analysis. Further topics include mass spectrometry in organic geochemistry, applications in geochronology and cosmochemistry, and organic mass spectrometry.

  15. Comparison of CID spectra of singly charged polypeptide antibiotic precursor ions obtained by positive-ion vacuum MALDI IT/RTOF and TOF/RTOF, AP-MALDI-IT and ESI-IT mass spectrometry.

    PubMed

    Pittenauer, Ernst; Zehl, Martin; Belgacem, Omar; Raptakis, Emmanuel; Mistrik, Robert; Allmaier, Günter

    2006-04-01

    Various classes of polypeptide antibiotics, including blocked linear peptides (gramicidin D), side-chain-cyclized peptides (bacitracin, viomycin, capreomycin), side-chain-cyclized depsipeptides (virginiamycin S), real cyclic peptides (tyrocidin, gramcidin S) and side-chain-cyclized lipopeptides (polymyxin B and E, amfomycin), were investigated by low-energy collision induced dissociation (LE-CID) as well as high-energy CID (HE-CID). Ion trap (IT) based instruments with different desorption/ionization techniques such as electrospray ionization (ESI), atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) and vacuum MALDI (vMALDI) as well as a vMALDI-time-of-flight (TOF)/curved field-reflectron instrument fitted with a gas collision cell were used. For optimum comparability of data from different IT instruments, the CID conditions were standardized and only singly charged precursor ions were considered. Additionally, HE-CID data obtained from the TOF-based instrument were acquired and compared with LE-CID data from ITs. Major differences between trap-based and TOF-based CID data are that the latter data set lacks abundant additional loss of small neutrals (e.g. ammonia, water) but contains product ions down to the immonium-ion-type region, thereby allowing the detection of even single amino-acid (even unusual amino acids) substitutions. For several polypeptide antibiotics, mass spectrometric as well as tandem mass spectrometric data are shown and discussed for the first time, and some yet undescribed minor components are also reported. De novo sequencing of unusually linked minor components of (e.g. cyclic) polypeptides is practically impossible without knowledge of the exact structure and fragmentation behavior of the major components. Finally, the described standardized CID condition constitutes a basic prerequisite for creating a searchable, annotated MS(n)-database of bioactive compounds. The applied desorption/ionization techniques showed no

  16. Idiopathic acquired dacryocystocele treated with endonasal endoscopic dacryocystorhinostomy

    PubMed Central

    Koltsidopoulos, Petros; Papageorgiou, Elena; Konidaris, Vasileios Efstathios; Skoulakis, Charalambos

    2013-01-01

    A 64-year-old woman presented with a medial canthal mass in her left eye, which was accompanied only by mild epiphora. There was no history of dacryocystitis, bloody tears, midfacial trauma or surgery. Physical examination showed a non-inflammatory, subcutaneous, immobile mass below the level of the medial canthal tendon. Lacrimal irrigation demonstrated blockage at the nasolacrimal duct. A CT revealed a non-enhancing, low density, cystic lesion in the inferomedial aspect of the left orbit without bony erosion, which was compatible with an idiopathic acquired dacryocystocele. The patient underwent endonasal endoscopic dacryocystorhinostomy (DCR) and silicone intubation. Epiphora resolved immediately after surgery. Two years after surgery, the patient has had no recurrence of either the epiphora or the orbital. Idiopathic acquired dacryocystocele associated only with epiphora without accompanying dacryocystitis although rare should be considered in the differential diagnosis of acquired non-inflammatory medial canthal masses. Endonasal endoscopic DCR represents a safe and effective treatment. PMID:23960153

  17. High-Speed Tandem Mass Spectrometric in Situ Imaging by Nanospray Desorption Electrospray Ionization Mass Spectrometry

    SciTech Connect

    Lanekoff, Ingela T.; Burnum-Johnson, Kristin E.; Thomas, Mathew; Short, Joshua TL; Carson, James P.; Cha, Jeeyeon; Dey, Sudhansu K.; Yang, Pengxiang; Prieto Conaway, Maria C.; Laskin, Julia

    2013-10-15

    Nanospray desorption electrospray ionization (nano-DESI) combined with tandem mass spectrometry (MS/MS), high-resolution mass analysis (m/m=17,500 at m/z 200), and rapid spectral acquisition enabled simultaneous imaging and identification of more than 300 molecules from 92 selected m/z windows (± 1 Da) with a spatial resolution of better than 150 um. Uterine sections of implantation sites on day 6 of pregnancy were analyzed in the ambient environment without any sample pre-treatment. MS/MS imaging was performed by scanning the sample under the nano-DESI probe at 10 um/s while acquiring higher-energy collision-induced dissociation (HCD) spectra for a targeted inclusion list of 92 m/z values at a rate of ~6.3 spectra/s. Molecular ions and their corresponding fragments, separated using high-resolution mass analysis, were assigned based on accurate mass measurement. Using this approach, we were able to identify and image both abundant and low-abundance isobaric species within each m/z window. MS/MS analysis enabled efficient separation and identification of isobaric sodium and potassium adducts of phospholipids. Furthermore, we identified several metabolites associated with early pregnancy and obtained the first 2D images of these molecules.

  18. Acquired Equivalence Changes Stimulus Representations

    ERIC Educational Resources Information Center

    Meeter, M.; Shohamy, D.; Myers, C. E.

    2009-01-01

    Acquired equivalence is a paradigm in which generalization is increased between two superficially dissimilar stimuli (or antecedents) that have previously been associated with similar outcomes (or consequents). Several possible mechanisms have been proposed, including changes in stimulus representations, either in the form of added associations or…

  19. 12 CFR 583.1 - Acquire.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... AND LOAN HOLDING COMPANIES § 583.1 Acquire. The term acquire means to acquire, directly or indirectly, ownership or control through an acquisition of shares, an acquisition of assets or assumption of...

  20. 12 CFR 583.1 - Acquire.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... AND LOAN HOLDING COMPANIES § 583.1 Acquire. The term acquire means to acquire, directly or indirectly, ownership or control through an acquisition of shares, an acquisition of assets or assumption of...

  1. 12 CFR 583.1 - Acquire.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... AND LOAN HOLDING COMPANIES § 583.1 Acquire. The term acquire means to acquire, directly or indirectly, ownership or control through an acquisition of shares, an acquisition of assets or assumption of...

  2. 12 CFR 583.1 - Acquire.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... AND LOAN HOLDING COMPANIES § 583.1 Acquire. The term acquire means to acquire, directly or indirectly, ownership or control through an acquisition of shares, an acquisition of assets or assumption of...

  3. Photographic spectra of fireballs

    NASA Astrophysics Data System (ADS)

    Borovička, J.

    2016-01-01

    Two methods of spectroscopy of meteors using image intensified video cameras and classical photographic film cameras are compared. Video cameras provide large number of low resolution spectra of meteors of normal brightness, which can be used for statistical studies. Large format film cameras have been used through the history and provide high resolution spectra, which can be used to derive temperature, density and absolute abundances of various elements in the radiating plasma. The sensitivity of films is, however, low and only spectra of bright meteors (fireballs) can be studied. Examples of photographic fireball spectra are provided.

  4. Spectra of stable sonoluminescence

    NASA Astrophysics Data System (ADS)

    Lewis, Stephen D.

    1992-12-01

    The continuous emission of picosecond pulses of light has been observed to originate from a bubble trapped at the pressure antinode of a resonant sound field in water and in water/glycerin mixtures. The spectra of this light in several solutions has been measured with a scanning monochrometer/photomultiplier detector system. The spectra are broadband and show strong emission in the UV region. A comparison of this measurement to two other independently produced spectra is made. The spectra are also modeled by a blackbody radiation distribution to determine an effective blackbody temperature and a size is deduced as if Sonoluminescence were characterized by blackbody radiation.

  5. Crack spectra analysis

    SciTech Connect

    Tiernan, M.

    1980-09-01

    Crack spectra derived from velocity data have been shown to exhibit systematics which reflect microstructural and textural differences between samples (Warren and Tiernan, 1980). Further research into both properties and information content of crack spectra have yielded the following: Spectral features are reproducible even at low pressures; certain observed spectral features may correspond to non-in-situ crack populations created during sample retrieval; the functional form of a crack spectra may be diagnostic of the sample's grain texture; hysteresis is observed in crack spectra between up and down pressure runs - it may be due to friction between the faces of closed crack populations.

  6. Acquired Aplastic Anemia in Children

    PubMed Central

    Hartung, Helge D.; Olson, Timothy S.; Bessler, Monica

    2013-01-01

    SYNOPSIS This article provides a practice-based and concise review of the etiology, diagnosis, and management of acquired aplastic anemia in children. Bone marrow transplantation, immunosuppressive therapy, and supportive care are discussed in detail. The aim is to provide the clinician with a better understanding of the disease and to offer guidelines for the management of children with this uncommon yet serious disorder. PMID:24237973

  7. Emotional attention in acquired prosopagnosia.

    PubMed

    Peelen, Marius V; Lucas, Nadia; Mayer, Eugene; Vuilleumier, Patrik

    2009-09-01

    The present study investigated whether emotionally expressive faces guide attention and modulate fMRI activity in fusiform gyrus in acquired prosopagnosia. Patient PS, a pure case of acquired prosopagnosia with intact right middle fusiform gyrus, performed two behavioral experiments and a functional imaging experiment to address these questions. In a visual search task involving face stimuli, PS was faster to select the target face when it was expressing fear or happiness as compared to when it was emotionally neutral. In a change detection task, PS detected significantly more changes when the changed face was fearful as compared to when it was neutral. Finally, an fMRI experiment showed enhanced activation to emotionally expressive faces and bodies in right fusiform gyrus. In addition, PS showed normal body-selective activation in right fusiform gyrus, partially overlapping the fusiform face area. Together these behavioral and neuroimaging results show that attention was preferentially allocated to emotional faces in patient PS, as observed in healthy subjects. We conclude that systems involved in the emotional guidance of attention by facial expression can function normally in acquired prosopagnosia, and can thus be dissociated from systems involved in face identification.

  8. Acquired causes of intestinal malabsorption.

    PubMed

    van der Heide, F

    2016-04-01

    This review focuses on the acquired causes, diagnosis, and treatment of intestinal malabsorption. Intestinal absorption is a complex process that depends on many variables, including the digestion of nutrients within the intestinal lumen, the absorptive surface of the small intestine, the membrane transport systems, and the epithelial absorptive enzymes. Acquired causes of malabsorption are classified by focussing on the three phases of digestion and absorption: 1) luminal/digestive phase, 2) mucosal/absorptive phase, and 3) transport phase. Most acquired diseases affect the luminal/digestive phase. These include short bowel syndrome, extensive small bowel inflammation, motility disorders, and deficiencies of digestive enzymes or bile salts. Diagnosis depends on symptoms, physical examination, and blood and stool tests. There is no gold standard for the diagnosis of malabsorption. Further testing should be based on the specific clinical context and the suspected underlying disease. Therapy is directed at nutritional support by enteral or parenteral feeding and screening for and supplementation of deficiencies in vitamins and minerals. Early enteral feeding is important for intestinal adaptation in short bowel syndrome. Medicinal treatment options for diarrhoea in malabsorption include loperamide, codeine, cholestyramine, or antibiotics. PMID:27086886

  9. Thermal Infrared Spectra of Experimentally Shocked Basalt

    NASA Astrophysics Data System (ADS)

    Johnson, J. R.; Horz, F.

    2003-12-01

    We acquired thermal infrared (3-40 microns) emissivity and hemispherical reflectance spectra of experimentally shocked samples of a fine-grained basalt from Grand Falls, AZ to document the spectral effects of shock as a function of increasing shock pressures (17-57 GPa). This sample contains 25% pyroxene, 20% olivine, and 45% feldspar, making it a suitable analog to the Surface Type 1 (basalt) observed in Thermal Emission Spectrometer (TES) data of Mars. Reflectance data (3-14 microns) were acquired using a Nexus 470 FTIR spectrometer at the HIGP, University of Hawaii, and emission spectra (5-40 microns) were acquired using a Nicolet Nexus 670 emission spectrometer at Arizona State University. These data complement similar previous measurements of experimentally shocked plagioclase and pyroxene relevant to interpreting spectra provided by TES. The samples were shocked using the 25-mm barrel gun at Johnson Space Center and provided ~400 mg per sample. Large (2-10 mm) chips of recovered material were separated from the samples and washed to remove clinging fines, and the residual was powdered to provide a consistent grain size ( ˜20 microns). Spectra were obtained of both the chips and the powder samples. Results for the chips show a shift in band positions in the 900-1200 wavenumber (wn) region compared to unshocked samples, consistent with the structural degradation of feldspar and subsequent formation of maskelynite and glass. The development of a band near 460 wn at high pressures is also consistent with glass formation in feldspars. Conversely, absorptions related to pyroxene remain present even at high pressures, consistent with previous work. Results for the powders show little variations with increasing pressure except for the loss of minor transparency features in the 800-900 wn region. Additional visible/near-infrared (0.35-2.50 microns) measurements of the powdered basalt samples also will be acquired at the RELAB facility. Future work will include

  10. Action spectra again?

    PubMed

    Coohill, T P

    1991-11-01

    Action spectroscopy has a long history and is of central importance to photobiological studies. Action spectra were among the first assays to point to chlorophyll as the molecule most responsible for plant growth and to DNA as the genetic material. It is useful to construct action spectra early in the investigation of new areas of photobiological research in an attempt to determine the wavelength limits of the radiation region causing the studied response. But due to the severe absorption of ultraviolet (UV) radiation by biological samples, UV action spectra were first limited to small cells (bacteria and fungi). Advances in techniques (e.g. single cell culture) and analysis allowed accurate action spectra to be reported even for mammalian cells. But precise analytical action spectra are often difficult to obtain when large, pigmented, or groups of cells are investigated. Here some action spectra are limited in interpretation and merely supply a wavelength vs effect curve. When polychromatic sources are employed, the interpretation of action spectra is even more complex and formidable. But such polychromatic action spectra can be more directly related to ambient responses. Since precise action spectra usually require the completion of a relatively large number of careful experiments using somewhat sophisticated equipment over a range of at least six wavelengths, they are often not pursued. But they remain central to the elucidation of the effect being studied. The worldwide community has agreed that stratospheric ozone is depleting, with the possibility of a consequent rise in the amount of UV-B (290-320 nm) reaching the earth's surface. It is therefore essential that new action spectra be completed for UV-B effects on a large variety of responses of human, animal, and aquatic plant systems. Combining these action spectra with the known amounts of UV-B reaching the biosphere can give rise to solar UV effectiveness spectra that, in turn, can give rise to estimates

  11. Rapid authentication of Gastrodiae rhizoma by direct ionization mass spectrometry.

    PubMed

    Wong, Ho-Yi; Hu, Bin; So, Pui-Kin; Chan, Chi-On; Mok, Daniel Kam-Wah; Xin, Gui-Zhong; Li, Ping; Yao, Zhong-Ping

    2016-09-28

    In this study, direct ionization mass spectrometry (DI-MS) for rapid authentication of Gastrodiae rhizoma (known as Tianma in Chinese), a popular herbal medicine, has been developed. This method is rapid, simple and allows direct generation of characteristic mass spectra from the raw herbal medicines with the application of some solvents and a high voltage. The acquired DI-MS spectra showed that gastrodin, parishin B/parishin C and parishin, the major active components of Gastrodiae rhizoma, could be found only in genuine Gastrodiae rhizoma samples, but not in counterfeit samples, thus allowing rapid authentication of Gastrodiae rhizoma. Moreover, wild and cultivated Gastrodiae rhizoma could be classified and Gastrodiae rhizoma from different geographical locations could be differentiated based on their different intensity ratios of characteristic ions or principal component analysis (PCA). This method is simple, rapid, reproducible, and can be extended to analyze other herbal medicines. PMID:27619090

  12. Definitive Identification of Laribacter hongkongensis Acquired in the United States

    PubMed Central

    Quig, David; Block, Mary Ann; Schreckenberger, Paul C.

    2015-01-01

    Laribacter hongkongensis is a potential emerging pathogen associated with community-acquired gastroenteritis and traveler's diarrhea. We report the isolation of L. hongkongensis from the stool of a patient who had no history of travel outside the United States. The organism was identified by phenotypic tests, mass spectrometry, and gene sequencing. PMID:25948608

  13. Acquired Hearing Loss in Children.

    PubMed

    Kenna, Margaret A

    2015-12-01

    Hearing loss is the most common congenital sensory impairment. According to National Health and Nutrition Examination Survey data from 2001 to 2008, 20.3% of subjects aged greater than or equal to 12 had unilateral or bilateral hearing loss. The World Health Organization notes that, worldwide, there are 360 million people with disabling hearing loss, with 50% preventable. Although many hearing losses are acquired, many others are manifestations of preexisting conditions. The purpose of a pediatric hearing evaluation is to identify the degree and type of hearing loss and etiology and to outline a comprehensive strategy that supports language and social development and communication.

  14. The inhibition of acquired fear.

    PubMed

    Izquierdo, Iván; Cammarota, Martín; Vianna, Mónica M R; Bevilaqua, Lía R M

    2004-01-01

    A conditioned stimulus (CS) associated with a fearsome unconditioned stimulus (US) generates learned fear. Acquired fear is at the root of a variety of mental disorders, among which phobias, generalized anxiety, the posttraumatic stress disorder (PTSD) and some forms of depression. The simplest way to inhibit learned fear is to extinguish it, which is usually done by repeatedly presenting the CS alone, so that a new association, CS-"no US", will eventually overcome the previously acquired CS-US association. Extinction was first described by Pavlov as a form of "internal inhibition" and was recommended by Freud and Ferenczi in the 1920s (who called it "habituation") as the treatment of choice for phobic disorders. It is used with success till this day, often in association with anxiolytic drugs. Extinction has since then been applied, also successfully and also often in association with anxiolytics, to the treatment of panic, generalized anxiety disorders and, more recently, PTSD. Extinction of learned fear involves gene expression, protein synthesis, N-methyl-D-aspartate (NMDA) receptors and signaling pathways in the hippocampus and the amygdala at the time of the first CS-no US association. It can be enhanced by increasing the exposure to the "no US" component at the time of behavioral testing, to the point of causing the complete uninstallment of the original fear response. Some theorists have recently proposed that reiteration of the CS alone may induce a reconsolidation of the learned behavior instead of its extinction. Reconsolidation would preserve the original memory from the labilization induced by its retrieval. If true, this would of course be disastrous for the psychotherapy of fear-motivated disorders. Here we show that neither the CS nor retrieval cause anything remotely like reconsolidation, but just extinction. In fact, our findings indicate that the reconsolidation hypothesis is essentially incorrect, at least for the form of contextual fear most

  15. Applying Tandem Mass Spectral Libraries for Solving the Critical Assessment of Small Molecule Identification (CASMI) LC/MS Challenge 2012.

    PubMed

    Oberacher, Herbert

    2013-01-01

    The "Critical Assessment of Small Molecule Identification" (CASMI) contest was aimed in testing strategies for small molecule identification that are currently available in the experimental and computational mass spectrometry community. We have applied tandem mass spectral library search to solve Category 2 of the CASMI Challenge 2012 (best identification for high resolution LC/MS data). More than 230,000 tandem mass spectra part of four well established libraries (MassBank, the collection of tandem mass spectra of the "NIST/NIH/EPA Mass Spectral Library 2012", METLIN, and the 'Wiley Registry of Tandem Mass Spectral Data, MSforID') were searched. The sample spectra acquired in positive ion mode were processed. Seven out of 12 challenges did not produce putative positive matches, simply because reference spectra were not available for the compounds searched. This suggests that to some extent the limited coverage of chemical space with high-quality reference spectra is still a problem encountered in tandem mass spectral library search. Solutions were submitted for five challenges. Three compounds were correctly identified (kanamycin A, benzyldiphenylphosphine oxide, and 1-isopropyl-5-methyl-1H-indole-2,3-dione). In the absence of any reference spectrum, a false positive identification was obtained for 1-aminoanthraquinone by matching the corresponding sample spectrum to the structurally related compounds N-phenylphthalimide and 2-aminoanthraquinone. Another false positive result was submitted for 1H-benz[g]indole; for the 1H-benz[g]indole-specific sample spectra provided, carbazole was listed as the best matching compound. In this case, the quality of the available 1H-benz[g]indole-specific reference spectra was found to hamper unequivocal identification.

  16. Thermodynamic analysis of spectra

    SciTech Connect

    Mitchell, G. E.; Shriner, J. F. Jr.

    2008-04-04

    Although random matrix theory had its initial application to neutron resonances, there is a relative scarcity of suitable nuclear data. The primary reason for this is the sensitivity of the standard measures used to evaluate spectra--the spectra must be essential pure (no state with a different symmetry) and complete (no states missing). Additional measures that are less sensitive to these experimental limitations are of significant value. The standard measure for long range order is the {delta}{sub 3} statistic. In the original paper that introduced this statistic, Dyson and Mehta also attempted to evaluate spectra with thermodynamic variables obtained from the circular orthogonal ensemble. We consider the thermodynamic 'internal energy' and evaluate its sensitivity to experimental limitations such as missing and spurious levels. Monte Carlo simulations suggest that the internal energy is less sensitive to mistakes than is {delta}{sub 3}, and thus the internal energy can serve as a addition to the tool kit for evaluating experimental spectra.

  17. Quantum synchrotron spectra from semirelativistic electrons in teragauss magnetic fields

    NASA Technical Reports Server (NTRS)

    Brainerd, J. J.

    1987-01-01

    Synchrotron spectra are calculated from quantum electrodynamic transition rates for thermal and power-law electron distributions. It is shown that quantum effects appear in thermal spectra when the photon energy is greater than the electron temperature, and in power-law spectra when the electron energy in units of the electron rest mass times the magnetic field strength in units of the critical field strength is of order unity. These spectra are compared with spectra calculated from the ultrarelativistic approximation for synchrotron emission. It is found that the approximation for the power-law spectra is good, and the approximation for thermal spectra produces the shape of the spectrum accurately but fails to give the correct normalization. Single photon pair creation masks the quantum effects for power-law distributions, so only modifications to thermal spectra are important for gamma-ray bursts.

  18. Malaria acquired in Haiti - 2010.

    PubMed

    2010-03-01

    On January 12, 2010, a 7.0 magnitude earthquake struck Haiti, which borders the Dominican Republic on the island of Hispaniola. The earthquake's epicenter was 10 miles west of the Haiti capital city of Port-au-Prince (estimated population: 2 million). According to the Haitian government, approximately 200,000 persons were killed, and 500,000 were left homeless. Malaria caused by Plasmodium falciparum infection is endemic in Haiti, and the principal mosquito vector is Anopheles albimanus, which frequently bites outdoors. Thus, displaced persons living outdoors or in temporary shelters and thousands of emergency responders in Haiti are at substantial risk for malaria. During January 12-February 25, CDC received reports of 11 laboratory-confirmed cases of P. falciparum malaria acquired in Haiti. Patients included seven U.S. residents who were emergency responders, three Haitian residents, and one U.S. traveler. This report summarizes the 11 cases and provides chemoprophylactic and additional preventive recommendations to minimize the risk for acquiring malaria for persons traveling to Haiti.

  19. Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID).

    PubMed

    Kelstrup, Christian D; Frese, Christian; Heck, Albert J R; Olsen, Jesper V; Nielsen, Michael L

    2014-08-01

    Unambiguous identification of tandem mass spectra is a cornerstone in mass-spectrometry-based proteomics. As the study of post-translational modifications (PTMs) by means of shotgun proteomics progresses in depth and coverage, the ability to correctly identify PTM-bearing peptides is essential, increasing the demand for advanced data interpretation. Several PTMs are known to generate unique fragment ions during tandem mass spectrometry, the so-called diagnostic ions, which unequivocally identify a given mass spectrum as related to a specific PTM. Although such ions offer tremendous analytical advantages, algorithms to decipher MS/MS spectra for the presence of diagnostic ions in an unbiased manner are currently lacking. Here, we present a systematic spectral-pattern-based approach for the discovery of diagnostic ions and new fragmentation mechanisms in shotgun proteomics datasets. The developed software tool is designed to analyze large sets of high-resolution peptide fragmentation spectra independent of the fragmentation method, instrument type, or protease employed. To benchmark the software tool, we analyzed large higher-energy collisional activation dissociation datasets of samples containing phosphorylation, ubiquitylation, SUMOylation, formylation, and lysine acetylation. Using the developed software tool, we were able to identify known diagnostic ions by comparing histograms of modified and unmodified peptide spectra. Because the investigated tandem mass spectra data were acquired with high mass accuracy, unambiguous interpretation and determination of the chemical composition for the majority of detected fragment ions was feasible. Collectively we present a freely available software tool that allows for comprehensive and automatic analysis of analogous product ions in tandem mass spectra and systematic mapping of fragmentation mechanisms related to common amino acids.

  20. 17 CFR 210.8-06 - Real estate operations acquired or to be acquired.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... Statements of Smaller Reporting Companies § 210.8-06 Real estate operations acquired or to be acquired. If, during the period for which income statements are required, the smaller reporting company has acquired... acquired or to be acquired. 210.8-06 Section 210.8-06 Commodity and Securities Exchanges SECURITIES...

  1. Lymphoma in acquired generalized lipodystrophy.

    PubMed

    Brown, Rebecca J; Chan, Jean L; Jaffe, Elaine S; Cochran, Elaine; DePaoli, Alex M; Gautier, Jean-Francois; Goujard, Cecile; Vigouroux, Corinne; Gorden, Phillip

    2016-01-01

    Acquired generalized lipodystrophy (AGL) is a rare disease thought to result from autoimmune destruction of adipose tissue. Peripheral T-cell lymphoma (PTCL) has been reported in two AGL patients. We report five additional cases of lymphoma in AGL, and analyze the role of underlying autoimmunity and recombinant human leptin (metreleptin) replacement in lymphoma development. Three patients developed lymphoma during metreleptin treatment (two PTCL and one ALK-positive anaplastic large cell lymphoma), and two developed lymphomas (mycosis fungoides and Burkitt lymphoma) without metreleptin. AGL is associated with high risk for lymphoma, especially PTCL. Autoimmunity likely contributes to this risk. Lymphoma developed with or without metreleptin, suggesting metreleptin does not directly cause lymphoma development; a theoretical role of metreleptin in lymphoma progression remains possible. For most patients with AGL and severe metabolic complications, the proven benefits of metreleptin on metabolic disease will likely outweigh theoretical risks of metreleptin in lymphoma development or progression.

  2. 7 CFR 926.10 - Acquire.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... REQUIREMENTS APPLICABLE TO CRANBERRIES NOT SUBJECT TO THE CRANBERRY MARKETING ORDER § 926.10 Acquire. Acquire means to obtain cranberries by any means whatsoever for the purpose of handling cranberries....

  3. 7 CFR 926.10 - Acquire.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... REQUIREMENTS APPLICABLE TO CRANBERRIES NOT SUBJECT TO THE CRANBERRY MARKETING ORDER § 926.10 Acquire. Acquire means to obtain cranberries by any means whatsoever for the purpose of handling cranberries....

  4. 7 CFR 926.10 - Acquire.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... REQUIREMENTS APPLICABLE TO CRANBERRIES NOT SUBJECT TO THE CRANBERRY MARKETING ORDER § 926.10 Acquire. Acquire means to obtain cranberries by any means whatsoever for the purpose of handling cranberries....

  5. 7 CFR 926.10 - Acquire.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... REQUIREMENTS APPLICABLE TO CRANBERRIES NOT SUBJECT TO THE CRANBERRY MARKETING ORDER § 926.10 Acquire. Acquire means to obtain cranberries by any means whatsoever for the purpose of handling cranberries....

  6. 7 CFR 926.10 - Acquire.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... REQUIREMENTS APPLICABLE TO CRANBERRIES NOT SUBJECT TO THE CRANBERRY MARKETING ORDER § 926.10 Acquire. Acquire means to obtain cranberries by any means whatsoever for the purpose of handling cranberries....

  7. 12 CFR 583.1 - Acquire.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... AND LOAN HOLDING COMPANIES § 583.1 Acquire. The term acquire means to acquire, directly or indirectly, ownership or control through an acquisition of shares, an acquisition of assets or assumption of liabilities, a merger or consolidation, or any similar transaction....

  8. Humidity affects relative ion abundance in direct analysis in real time mass spectrometry of hexamethylene triperoxide diamine.

    PubMed

    Newsome, G Asher; Ackerman, Luke K; Johnson, Kevin J

    2014-12-16

    Unstable explosive hexamethylene triperoxide diamine (HMTD) is dangerous in quantity and benefits from the minimal sampling handling associated with atmospheric pressure chemical ionization for mass spectral analysis. Seasonal variation observed in HMTD mass spectra suggested a humidity dependence. Therefore, direct analysis in real time (DART) ionization mass spectra were acquired at a range of humidity values. An enclosure was designed to fit around the ion source and mass spectrometer inlet at atmospheric pressure. The enclosure was supplied with controlled amounts of humidified air from a test atmosphere generator to create programmable conditions for ambient analysis. The relative abundance and fragmentation of analyte ions were observed to change reliably with changing humidity values and, to a lesser degree, temperature. Humidity at such plasma-based ion sources should be regulated to avoid ∼90% shifts in relative ion abundance and provide stability and reproducibility of HMTD analysis.

  9. Atomic Spectra Database (ASD)

    National Institute of Standards and Technology Data Gateway

    SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access)   This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.

  10. MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications.

    PubMed

    McCloskey, Douglas; Young, Jamey D; Xu, Sibei; Palsson, Bernhard O; Feist, Adam M

    2016-01-19

    The analytical challenges to acquire accurate isotopic data of intracellular metabolic intermediates for stationary, nonstationary, and dynamic metabolic flux analysis (MFA) are numerous. This work presents MID Max, a novel LC-MS/MS workflow, acquisition, and isotopomer deconvolution method for MFA that takes advantage of additional scan types that maximizes the number of mass isotopomer distributions (MIDs) that can be acquired in a given experiment. The analytical method was found to measure the MIDs of 97 metabolites, corresponding to 74 unique metabolite-fragment pairs (32 precursor spectra and 42 product spectra) with accuracy and precision. The compounds measured included metabolic intermediates in central carbohydrate metabolism and cofactors of peripheral metabolism (e.g., ATP). Using only a subset of the acquired MIDs, the method was found to improve the precision of flux estimations and number of resolved exchange fluxes for wild-type E. coli compared to traditional methods and previously published data sets.

  11. Associative Learning Through Acquired Salience.

    PubMed

    Treviño, Mario

    2015-01-01

    Most associative learning studies describe the salience of stimuli as a fixed learning-rate parameter. Presumptive saliency signals, however, have also been linked to motivational and attentional processes. An interesting possibility, therefore, is that discriminative stimuli could also acquire salience as they become powerful predictors of outcomes. To explore this idea, we first characterized and extracted the learning curves from mice trained with discriminative images offering varying degrees of structural similarity. Next, we fitted a linear model of associative learning coupled to a series of mathematical representations for stimulus salience. We found that the best prediction, from the set of tested models, was one in which the visual salience depended on stimulus similarity and a non-linear function of the associative strength. Therefore, these analytic results support the idea that the net salience of a stimulus depends both on the items' effective salience and the motivational state of the subject that learns about it. Moreover, this dual salience model can explain why learning about a stimulus not only depends on the effective salience during acquisition but also on the specific learning trajectory that was used to reach this state. Our mathematical description could be instrumental for understanding aberrant salience acquisition under stressful situations and in neuropsychiatric disorders like schizophrenia, obsessive-compulsive disorder, and addiction.

  12. Infections Acquired in the Garden.

    PubMed

    Cunha, Cheston B; Cunha, Burke A

    2015-10-01

    Gardening is a wonderful pastime, and the garden is a very peaceful place to enjoy one's vacation. However, the garden may be a treacherous place for very young or compromised hosts when one takes into account the infectious potential residing in the soil, as well as the insect vectors on plants and animals. Even normal hosts may acquire a variety of infections from the soil, animals, or animal-related insect bites. The location of the garden, its natural animal and insect inhabitants, and the characteristics of the soil play a part in determining its infectious potential. The most important factor making the garden an infectious and dangerous place is the number and interaction of animals, whether they are pets or wild, that temporarily use the garden for part of their daily activities. The clinician should always ask about garden exposure, which will help in eliminating the diagnostic possibilities for the patient. The diagnostic approach is to use epidemiological principles in concert with clinical clues, which together should suggest a reasonable list of diagnostic possibilities. Organ involvement and specific laboratory tests help further narrow the differential diagnosis and determine the specific tests necessary to make a definitive diagnosis. PMID:26542044

  13. Inherited or acquired metabolic disorders.

    PubMed

    Eichler, Florian; Ratai, Eva; Carroll, Jason J; Masdeu, Joseph C

    2016-01-01

    This chapter starts with a description of imaging of inherited metabolic disorders, followed by a discussion on imaging of acquired toxic-metabolic disorders of the adult brain. Neuroimaging is crucial for the diagnosis and management of a number of inherited metabolic disorders. Among these, inherited white-matter disorders commonly affect both the nervous system and endocrine organs. Magnetic resonance imaging (MRI) has enabled new classifications of these disorders that have greatly enhanced both our diagnostic ability and our understanding of these complex disorders. Beyond the classic leukodystrophies, we are increasingly recognizing new hereditary leukoencephalopathies such as the hypomyelinating disorders. Conventional imaging can be unrevealing in some metabolic disorders, but proton magnetic resonance spectroscopy (MRS) may be able to directly visualize the metabolic abnormality in certain disorders. Hence, neuroimaging can enhance our understanding of pathogenesis, even in the absence of a pathologic specimen. This review aims to present pathognomonic brain MRI lesion patterns, the diagnostic capacity of proton MRS, and information from clinical and laboratory testing that can aid diagnosis. We demonstrate that applying an advanced neuroimaging approach enhances current diagnostics and management. Additional information on inherited and metabolic disorders of the brain can be found in Chapter 63 in the second volume of this series. PMID:27432685

  14. Infections Acquired in the Garden.

    PubMed

    Cunha, Cheston B; Cunha, Burke A

    2015-10-01

    Gardening is a wonderful pastime, and the garden is a very peaceful place to enjoy one's vacation. However, the garden may be a treacherous place for very young or compromised hosts when one takes into account the infectious potential residing in the soil, as well as the insect vectors on plants and animals. Even normal hosts may acquire a variety of infections from the soil, animals, or animal-related insect bites. The location of the garden, its natural animal and insect inhabitants, and the characteristics of the soil play a part in determining its infectious potential. The most important factor making the garden an infectious and dangerous place is the number and interaction of animals, whether they are pets or wild, that temporarily use the garden for part of their daily activities. The clinician should always ask about garden exposure, which will help in eliminating the diagnostic possibilities for the patient. The diagnostic approach is to use epidemiological principles in concert with clinical clues, which together should suggest a reasonable list of diagnostic possibilities. Organ involvement and specific laboratory tests help further narrow the differential diagnosis and determine the specific tests necessary to make a definitive diagnosis.

  15. Associative Learning Through Acquired Salience

    PubMed Central

    Treviño, Mario

    2016-01-01

    Most associative learning studies describe the salience of stimuli as a fixed learning-rate parameter. Presumptive saliency signals, however, have also been linked to motivational and attentional processes. An interesting possibility, therefore, is that discriminative stimuli could also acquire salience as they become powerful predictors of outcomes. To explore this idea, we first characterized and extracted the learning curves from mice trained with discriminative images offering varying degrees of structural similarity. Next, we fitted a linear model of associative learning coupled to a series of mathematical representations for stimulus salience. We found that the best prediction, from the set of tested models, was one in which the visual salience depended on stimulus similarity and a non-linear function of the associative strength. Therefore, these analytic results support the idea that the net salience of a stimulus depends both on the items' effective salience and the motivational state of the subject that learns about it. Moreover, this dual salience model can explain why learning about a stimulus not only depends on the effective salience during acquisition but also on the specific learning trajectory that was used to reach this state. Our mathematical description could be instrumental for understanding aberrant salience acquisition under stressful situations and in neuropsychiatric disorders like schizophrenia, obsessive-compulsive disorder, and addiction. PMID:26793078

  16. Associative Learning Through Acquired Salience.

    PubMed

    Treviño, Mario

    2015-01-01

    Most associative learning studies describe the salience of stimuli as a fixed learning-rate parameter. Presumptive saliency signals, however, have also been linked to motivational and attentional processes. An interesting possibility, therefore, is that discriminative stimuli could also acquire salience as they become powerful predictors of outcomes. To explore this idea, we first characterized and extracted the learning curves from mice trained with discriminative images offering varying degrees of structural similarity. Next, we fitted a linear model of associative learning coupled to a series of mathematical representations for stimulus salience. We found that the best prediction, from the set of tested models, was one in which the visual salience depended on stimulus similarity and a non-linear function of the associative strength. Therefore, these analytic results support the idea that the net salience of a stimulus depends both on the items' effective salience and the motivational state of the subject that learns about it. Moreover, this dual salience model can explain why learning about a stimulus not only depends on the effective salience during acquisition but also on the specific learning trajectory that was used to reach this state. Our mathematical description could be instrumental for understanding aberrant salience acquisition under stressful situations and in neuropsychiatric disorders like schizophrenia, obsessive-compulsive disorder, and addiction. PMID:26793078

  17. THIRTY NEW LOW-MASS SPECTROSCOPIC BINARIES

    SciTech Connect

    Shkolnik, Evgenya L.; Hebb, Leslie; Cameron, Andrew C.; Liu, Michael C.; Neill Reid, I. E-mail: Andrew.Cameron@st-and.ac.u E-mail: mliu@ifa.hawaii.ed

    2010-06-20

    As part of our search for young M dwarfs within 25 pc, we acquired high-resolution spectra of 185 low-mass stars compiled by the NStars project that have strong X-ray emission. By cross-correlating these spectra with radial velocity standard stars, we are sensitive to finding multi-lined spectroscopic binaries. We find a low-mass spectroscopic binary fraction of 16% consisting of 27 SB2s, 2 SB3s, and 1 SB4, increasing the number of known low-mass spectroscopic binaries (SBs) by 50% and proving that strong X-ray emission is an extremely efficient way to find M-dwarf SBs. WASP photometry of 23 of these systems revealed two low-mass eclipsing binaries (EBs), bringing the count of known M-dwarf EBs to 15. BD-22 5866, the ESB4, was fully described in 2008 by Shkolnik et al. and CCDM J04404+3127 B consists of two mid-M stars orbiting each other every 2.048 days. WASP also provided rotation periods for 12 systems, and in the cases where the synchronization time scales are short, we used P{sub rot} to determine the true orbital parameters. For those with no P{sub rot}, we used differential radial velocities to set upper limits on orbital periods and semimajor axes. More than half of our sample has near-equal-mass components (q > 0.8). This is expected since our sample is biased toward tight orbits where saturated X-ray emission is due to tidal spin-up rather than stellar youth. Increasing the samples of M-dwarf SBs and EBs is extremely valuable in setting constraints on current theories of stellar multiplicity and evolution scenarios for low-mass multiple systems.

  18. NIMS Radiance Point Spectra of Gaspra V1.0

    NASA Astrophysics Data System (ADS)

    Granahan, J. C.

    2014-10-01

    This data volume contains radiometrically corrected point spectra of asteroid 951 as acquired by the Galileo spacecraft Near Infrared Mapping Spectrometer (NIMS) on October 29, 1991. They record the spectra collected as the Galileo spacecraft approached the target asteroid. These data are products of the calibration of the raw data number files gap015tn.qub, gap035tn.qub, gap036tn.qub, gap037tn.qub, and gap038tn.qub (DATA SET ID ='GO-A-NIMS-3 TUBE-V1.0') with calibration factors acquired during the first Earth/Moon encounter of the Galileo mission. These raw data .qub files are archived in the Imaging Node of the NASA Planetary Data System (PDS). The calibrated spectra consist of radiance measurements for wavelengths between 0.7 - 5.2 micrometers.

  19. Clinicopathological associations of acquired erythroblastopenia

    PubMed Central

    Gunes, Gursel; Malkan, Umit Yavuz; Yasar, Hatime Arzu; Eliacik, Eylem; Haznedaroglu, Ibrahim Celalettin; Demiroglu, Haluk; Sayinalp, Nilgun; Aksu, Salih; Etgul, Sezgin; Aslan, Tuncay; Goker, Hakan; Ozcebe, Osman Ilhami; Buyukasik, Yahya

    2015-01-01

    Introduction: Acquired erythroblastopenia (AE) is a rare clinical situation. It is characterized by the reduction of erythroid precursors in the bone marrow together with the low reticulocyte counts in the peripheral blood. Background: Main secondary causes of AE are drugs, Parvovirus B19 and other infectious reasons, lymphoid and myeloid neoplasia, autoimmune diseases, thymoma and pregnancy. The aim of this study is to assess the frequencies and clinical associations of AE via analyzing 12340 bone marrow samples in a retrospective manner. Material and method: Bone marrow aspirations which were obtained from patients who applied to Hacettepe University Hematology Clinic between 2002 and 2013, were analyzed retrospectively. Results: Thirty four erythroblastopenia cases were found. Patients ranged in age from 16 to 80 years with a median of 38 years. Fifteen patients were men (44%) and nineteen were women (56%). In these patients, detected causes of erythroblastopenia were MDS, idiopathic pure red cell aplasia (PRCA), parvovirus infection, post chemotherapy aplasia, plasma proliferative diseases, copper deficiency due to secondary amyloidosis, fever of unknown origin, hemophagocytic syndrome, enteric fever and legionella pneumonia. We found that between those reasons the most common causes of erythroblastopenia are MDS (17.7%) and idiopathic PRCA (17.7%). Discussion: As a result, erythroblastopenia in the bone marrow may be an early sign of MDS. In those AE cases possibility of being MDS must be kept in mind as it can be mistaken for PRCA. Conclusion: To conclude, in adults MDS without excess blast is one of the most common causes of erythroblastopenia in clinical practice and in case of erythroblastopenia the presence of MDS should be investigated. PMID:26885236

  20. [Reflection on treatment of acquired immunodeficiency syndrome by integrative medicine].

    PubMed

    Wang, Dan-Ni

    2012-02-01

    The current situation of Chinese medicine and Western medicine treatment of acquired immunodeficiency syndrome (AIDS) has made the integrative medicine treatment of AIDS an important treatment strategy. Integrative medicine treatment of AIDS has made certain achievements in clinical research, basic research, and other aspects. It has good mass foundation and curative efficacy, as well as insufficiency. I hope integrative medicine can be brought into full play in the treatment of AIDS and make breakthrough progress.

  1. Consistent cosmic microwave background spectra from quantum depletion

    SciTech Connect

    Casadio, Roberto; Orlandi, Alessio; Kühnel, Florian E-mail: florian.kuhnel@fysik.su.se

    2015-09-01

    Following a new quantum cosmological model proposed by Dvali and Gomez, we quantitatively investigate possible modifications to the Hubble parameter and following corrections to the cosmic microwave background spectrum. In this model, scalar and tensor perturbations are generated by the quantum depletion of the background inflaton and graviton condensate respectively. We show how the inflaton mass affects the power spectra and the tensor-to-scalar ratio. Masses approaching the Planck scale would lead to strong deviations, while standard spectra are recovered for an inflaton mass much smaller than the Planck mass.

  2. Parmeterization of spectra

    NASA Technical Reports Server (NTRS)

    Cornish, C. R.

    1983-01-01

    Following reception and analog to digital conversion (A/D) conversion, atmospheric radar backscatter echoes need to be processed so as to obtain desired information about atmospheric processes and to eliminate or minimize contaminating contributions from other sources. Various signal processing techniques have been implemented at mesosphere-stratosphere-troposphere (MST) radar facilities to estimate parameters of interest from received spectra. Such estimation techniques need to be both accurate and sufficiently efficient to be within the capabilities of the particular data-processing system. The various techniques used to parameterize the spectra of received signals are reviewed herein. Noise estimation, electromagnetic interference, data smoothing, correlation, and the Doppler effect are among the specific points addressed.

  3. CHARACTERIZING THE COOL KOIs. VI. H- AND K-BAND SPECTRA OF KEPLER M DWARF PLANET-CANDIDATE HOSTS

    SciTech Connect

    Muirhead, Philip S.; Becker, Juliette; Price, Ellen M.; Thorp, Rachel; Riddle, Reed; Feiden, Gregory A.; Rojas-Ayala, Bárbara; Vanderburg, Andrew; Johnson, John Asher; Law, Nicholas M.; Baranec, Christoph; Hamren, Katherine; Schlawin, Everett; Lloyd, James P.; Covey, Kevin R.

    2014-07-01

    We present H- and K-band spectra for late-type Kepler Objects of Interest (the {sup C}ool KOIs{sup )}: low-mass stars with transiting-planet candidates discovered by NASA's Kepler Mission that are listed on the NASA Exoplanet Archive. We acquired spectra of 103 Cool KOIs and used the indices and calibrations of Rojas-Ayala et al. to determine their spectral types, stellar effective temperatures, and metallicities, significantly augmenting previously published values. We interpolate our measured effective temperatures and metallicities onto evolutionary isochrones to determine stellar masses, radii, luminosities, and distances, assuming the stars have settled onto the main sequence. As a choice of isochrones, we use a new suite of Dartmouth predictions that reliably include mid-to-late M dwarf stars. We identify five M4V stars: KOI-961 (confirmed as Kepler 42), KOI-2704, KOI-2842, KOI-4290, and the secondary component to visual binary KOI-1725, which we call KOI-1725 B. We also identify a peculiar star, KOI-3497, which has Na and Ca lines consistent with a dwarf star but CO lines consistent with a giant. Visible-wavelength adaptive optics imaging reveals two objects within a 1 arcsec diameter; however, the objects' colors are peculiar. The spectra and properties presented in this paper serve as a resource for prioritizing follow-up observations and planet validation efforts for the Cool KOIs and are all available for download online using the ''data behind the figure'' feature.

  4. Characterizing the Cool KOIs. VI. H- and K-band Spectra of Kepler M Dwarf Planet-candidate Hosts

    NASA Astrophysics Data System (ADS)

    Muirhead, Philip S.; Becker, Juliette; Feiden, Gregory A.; Rojas-Ayala, Bárbara; Vanderburg, Andrew; Price, Ellen M.; Thorp, Rachel; Law, Nicholas M.; Riddle, Reed; Baranec, Christoph; Hamren, Katherine; Schlawin, Everett; Covey, Kevin R.; Johnson, John Asher; Lloyd, James P.

    2014-07-01

    We present H- and K-band spectra for late-type Kepler Objects of Interest (the "Cool KOIs"): low-mass stars with transiting-planet candidates discovered by NASA's Kepler Mission that are listed on the NASA Exoplanet Archive. We acquired spectra of 103 Cool KOIs and used the indices and calibrations of Rojas-Ayala et al. to determine their spectral types, stellar effective temperatures, and metallicities, significantly augmenting previously published values. We interpolate our measured effective temperatures and metallicities onto evolutionary isochrones to determine stellar masses, radii, luminosities, and distances, assuming the stars have settled onto the main sequence. As a choice of isochrones, we use a new suite of Dartmouth predictions that reliably include mid-to-late M dwarf stars. We identify five M4V stars: KOI-961 (confirmed as Kepler 42), KOI-2704, KOI-2842, KOI-4290, and the secondary component to visual binary KOI-1725, which we call KOI-1725 B. We also identify a peculiar star, KOI-3497, which has Na and Ca lines consistent with a dwarf star but CO lines consistent with a giant. Visible-wavelength adaptive optics imaging reveals two objects within a 1 arcsec diameter; however, the objects' colors are peculiar. The spectra and properties presented in this paper serve as a resource for prioritizing follow-up observations and planet validation efforts for the Cool KOIs and are all available for download online using the "data behind the figure" feature.

  5. Barnacle Bill Spectra

    NASA Technical Reports Server (NTRS)

    1997-01-01

    These IMP spectra show the characteristics of the rock surface measured by the Alpha Proton X-Ray Spectrometer (blue), the soil trapped in pits on the rock surface (red), and the deposit of bright drift on the top of the rock. The area measured by the APXS has the properties expected for nearly unweathered igneous rock, and the soil trapped in the pits is intermediate to the unweathered rock and the highly weathered drift material.

  6. Building relationships between plant traits and leaf spectra to reduce uncertainty in terrestrial ecosystem models

    NASA Astrophysics Data System (ADS)

    Lieberman-Cribbin, W.; Rogers, A.; Serbin, S.; Ely, K.

    2015-12-01

    Despite climate projections, there is uncertainty in how terrestrial ecosystems will respond to warming temperatures and increased atmospheric carbon dioxide concentrations. Earth system models are used to determine how ecosystems will respond in the future, but there is considerable variation in how plant traits are represented within these models. A potential approach to reducing uncertainty is the establishment of spectra-trait linkages among plant species. These relationships allow the accurate estimation of biochemical characteristics of plants from their shortwave spectral profiles. Remote sensing approaches can then be implemented to acquire spectral data and estimate plant traits over large spatial and temporal scales. This paper describes a greenhouse experiment conducted at Brookhaven National Laboratory in which spectra-trait relationships were investigated for 8 different plant species. This research was designed to generate a broad gradient in plant traits, using a range of species grown in different sized pots with different soil type. Fertilizer was also applied in different amounts to generate variation in plant C and N status that will be reflected in the traits measured, as well as the spectra observed. Leaves were sampled at different developmental stages to increase variation. Spectra and plant traits were then measured and a partial least-squares regression (PLSR) modeling approach was used to establish spectra-trait relationships. Despite the variability in growing conditions and plant species, our PLSR models could be used to accurately estimate plant traits from spectral signatures, yielding model calibration R2 and root mean square error (RMSE) values, respectively, of 0.85 and 0.30 for percent nitrogen by mass (Nmass%), R2 0.78 and 0.75 for carbon to nitrogen (C:N) ratio, 0.87 and 2.39 for leaf mass area (LMA), and 0.76 R2 and 15.16 for water (H2O) content. This research forms the basis for establishing new and more comprehensive spectra

  7. Photoluminescence Spectroscopy of Mass-Selected Electrosprayed Ions Embedded in Cryogenic Rare-Gas Matrixes.

    PubMed

    Kern, Bastian; Greisch, Jean-François; Strelnikov, Dmitry; Weis, Patrick; Böttcher, Artur; Ruben, Mario; Schäfer, Bernhard; Schooss, Detlef; Kappes, Manfred M

    2015-12-01

    An apparatus is presented which combines nanoelectrospray ionization for isolation of large molecular ions from solution, mass-to-charge ratio selection in gas-phase, low-energy-ion-beam deposition into a (co-condensed) inert gas matrix and UV laser-induced visible-region photoluminescence (PL) of the matrix isolated ions. Performance is tested by depositing three different types of lanthanoid diketonate cations including also a dissociation product species not directly accessible by chemical synthesis. For these strongly photoluminescent ions, accumulation of some femto- to picomoles in a neon matrix (over a time scale of tens of minutes to several hours) is sufficient to obtain well-resolved dispersed emission spectra. We have ruled out contributions to these spectra due to charge neutralization or fragmentation during deposition by also acquiring photoluminescence spectra of the same ionic species in the gas phase. PMID:26553589

  8. The Quadrupole Mass Spectrometer

    ERIC Educational Resources Information Center

    Matheson, E.; Harris, T. J.

    1969-01-01

    Describes the construction and operation of a quadrupole mass spectrometer for experiments in an advanced-teaching laboratory. Discusses the theory of operation of the spectrometer and the factors affecting the resolution. Some examples of mass spectra obtained with this instrument are presented and discussed. (LC)

  9. IUE archived spectra

    NASA Technical Reports Server (NTRS)

    Sullivan, Edward C.; Bohlin, Ralph C.; Heap, Sara R.; West, Donald K.; Schmitz, Marion

    1988-01-01

    The International Ultraviolet Explorer (IUE) Satellite has been in continuous operation since January 26, 1978. To date, approximately 65,000 spectra have been stored in an archive at Goddard Space Flight Center in Greenbelt, MD. A number of procedures have been generated to facilitate access to the data in the IUE spectral archive. This document describes the procedures which include on-line quick look of the displays, search of an observation data base for selected observations, and several methods for ordering data from the archive.

  10. VARIABILITY IN OPTICAL SPECTRA OF {epsilon} ORIONIS

    SciTech Connect

    Thompson, Gregory B.; Morrison, Nancy D. E-mail: nmorris@utnet.utoledo.edu

    2013-04-15

    We present the results of a time series analysis of 130 echelle spectra of {epsilon} Ori (B0 Ia), acquired over seven observing seasons between 1998 and 2006 at Ritter Observatory. The equivalent widths of H{alpha} (net) and He I {lambda}5876 were measured and radial velocities were obtained from the central absorption of He I {lambda}5876. Temporal variance spectra (TVS) revealed significant wind variability in both H{alpha} and He I {lambda}5876. The He I TVS have a double-peaked profile consistent with radial velocity oscillations. A periodicity search was carried out on the equivalent width and radial velocity data, as well as on wavelength-binned spectra. This analysis has revealed several periods in the variability with timescales of two to seven days. Many of these periods exhibit sinusoidal modulation in the associated phase diagrams. Several of these periods were present in both H{alpha} and He I, indicating a possible connection between the wind and the photosphere. Due to the harmonic nature of these periods, stellar pulsations may be the origin of some of the observed variability. Periods on the order of the rotational period were also detected in the He I line in the 1998-1999 season and in both lines during the 2004-2005 season. These periods may indicate rotational modulation due to structure in the wind.

  11. Acquired Surface Dyslexia: The Evidence from Hebrew.

    ERIC Educational Resources Information Center

    Birnboim, Smadar

    1995-01-01

    Investigates the symptoms of acquired surface dyslexia in Hebrew. Four acquired surface dyslexic adults were compared with eight normal second graders in terms of reading strategy. Homophones and homographs were a major source of difficulty for native Hebrew surface dyslexic readers; the normal second graders used a non-lexical strategy. (45…

  12. Uncontrolled variability in the extinction spectra of C60 nanoparticle suspensions.

    PubMed

    Chang, Xiaojun; Vikesland, Peter J

    2013-08-01

    To properly investigate the environmental transport, fate, and impact of fullerene C60 nanoparticles (nC60), it is necessary to reproducibly obtain nC60 suspensions and to accurately determine their concentration ([C60]). The results in the present study, however, clearly illustrate that the production of nC60 via extended mixing and via sonication are highly stochastic top-down processes subject to widely divergent end points. nC60 suspensions exhibit variable characteristics (e.g., [C60], average particle size, size distribution, etc.) that make it challenging, if not impossible, to acquire reproducible UV-vis extinction spectra. The mass extinction coefficient, which is the absorptivity of a suspension with [C60] = 1 mM obtained by normalizing UV-vis spectra by the mass concentration of C60 in the suspension, decreases with a given suspension's hydrodynamic diameter, whereas the particle extinction coefficient, which is the absorptivity of a suspension containing one mole of nC60 nanoparticles with the same size distribution as the target suspension and calculated based upon the suspension nanoparticle size distribution, increases with its number weighted average diameter. Other spectroscopic properties of nC60 (e.g., absorbance bandwidth, position of absorption maximum, and relative extinction intensity) also change with average particle size. As a result of the extant variability between samples, when UV-vis spectra are employed to calculate or represent [C60] for fullerene nanoparticle suspensions, extreme care must be taken and other colloidal properties of this suspension must be measured to obtain an accurate result.

  13. Meteors and meteorites spectra

    NASA Astrophysics Data System (ADS)

    Koukal, J.; Srba, J.; Gorková, S.; Lenža, L.; Ferus, M.; Civiš, S.; Knížek, A.; Kubelík, P.; Kaiserová, T.; Váňa, P.

    2016-01-01

    The main goal of our meteor spectroscopy project is to better understand the physical and chemical properties of meteoroids. Astrometric and spectral observations of real meteors are obtained via spectroscopic CCD video systems. Processed meteor data are inserted to the EDMOND database (European viDeo MeteOr Network Database) together with spectral information. The fully analyzed atmospheric trajectory, orbit and also spectra of a Leonid meteor/meteoroid captured in November 2015 are presented as an example. At the same time, our target is the systematization of spectroscopic emission lines for the comparative analysis of meteor spectra. Meteoroid plasma was simulated in a laboratory by laser ablation of meteorites samples using an (ArF) excimer laser and the LIDB (Laser Induced Dielectric Breakdown) in a low pressure atmosphere and various gases. The induced plasma emissions were simultaneously observed with the Echelle Spectrograph and the same CCD video spectral camera as used for real meteor registration. Measurements and analysis results for few selected meteorite samples are presented and discussed.

  14. Matrix-assisted laser desorption/ionization mass spectrometry of neutral and acidic oligosaccharides with collision-induced dissociation.

    PubMed

    Mechref, Y; Baker, A G; Novotny, M V

    1998-12-15

    Using ribonuclease B and human alpha 1-acid glycoprotein (AGP) as model glycoproteins, matrix-assisted laser desorption/ionization (MALDI) mass spectrometry with collision-induced dissociation (CID) is validated here as an effective tool for oligosaccharide sequencing. The spectra acquired for high-mannose and complex oligosaccharide structures show characteristic fragments resulting from cleavages of the glycosidic bonds and a few cross-ring cleavages. Esterification of the sialic acid residues is essential in stabilizing the acidic N-linked oligosaccharides. An important analytical feature observed in all acquired spectra is the occurrence of cleavages on the same antenna up to the branching point, as deduced from the absence of fragmentation due to the simultaneous cleavages on two or more antennas.

  15. Fuzzy Logic Classification of Imaging Laser Desorption Fourier Transform Mass Spectrometry Data

    SciTech Connect

    Timothy R. McJunkin; Jill R. Scott

    2008-06-01

    The fuzzy logic method is applied to classification of mass spectra obtained with an imaging internal source Fourier transform mass spectrometer (I2LD-FTMS). Traditionally, an operator uses the relative abundance of ions with specific mass-to-charge (m/z) ratios to categorize spectra. An operator does this by comparing the spectrum of m/z versus abundance of an unknown sample against a library of spectra from known samples. Automated positioning and acquisition allow the I2LD-FTMS to acquire data from very large grids, which would require classification of up to 3600 spectra per hour to keep pace with the acquisition. The tedious job of classifying numerous spectra generated in an I2LD-FTMS imaging application can be replaced by a fuzzy rule base if the cues an operator uses can be encapsulated. Appropriate methods for assigning fuzzy membership values for inputs (e.g., mass spectrum abundances) and choice of fuzzy inference operators to translate linguistic antecedent into confidence values for the consequence (or in this case the classification) is followed by using the maximum confidence and a necessary minimum threshold for making a crisp decision. This paper also describes a method for gathering statistics on ions, which are not currently used in the rule base, but which may be candidates for making the rule base more accurate and complete or to form new rule bases based on data obtained from known samples. A spatial method for classifying spectra with low membership values, based on neighboring sample classifications, is also presented.

  16. Dose spectra from energetic particles and neutrons

    NASA Astrophysics Data System (ADS)

    Schwadron, Nathan; Bancroft, Chris; Bloser, Peter; Legere, Jason; Ryan, James; Smith, Sonya; Spence, Harlan; Mazur, Joe; Zeitlin, Cary

    2013-10-01

    spectra from energetic particles and neutrons (DoSEN) are an early-stage space technology research project that combines two advanced complementary radiation detection concepts with fundamental advantages over traditional dosimetry. DoSEN measures not only the energy but also the charge distribution (including neutrons) of energetic particles that affect human (and robotic) health in a way not presently possible with current dosimeters. For heavy ions and protons, DoSEN provides a direct measurement of the lineal energy transfer (LET) spectra behind shielding material. For LET measurements, DoSEN contains stacks of thin-thick Si detectors similar in design to those used for the Cosmic Ray Telescope for the Effects of Radiation. With LET spectra, we can now directly break down the observed spectrum of radiation into its constituent heavy-ion components and through biologically based quality factors that provide not only doses and dose rates but also dose equivalents, associated rates, and even organ doses. DoSEN also measures neutrons from 10 to 100 MeV, which requires enough sensitive mass to fully absorb recoil particles that the neutrons produce. DoSEN develops the new concept of combining these independent measurements and using the coincidence of LET measurements and neutron detection to significantly reduce backgrounds in each measurement. The background suppression through the use of coincidence allows for significant reductions in size, mass, and power needed to provide measurements of dose, neutron dose, dose equivalents, LET spectra, and organ doses. Thus, we introduce the DoSEN concept: a promising low-mass instrument that detects the full spectrum of energetic particles, heavy ions, and neutrons to determine biological impact of radiation in space.

  17. Continuum Fitting HST QSO Spectra

    NASA Technical Reports Server (NTRS)

    Tytler, David; Oliversen, Ronald J. (Technical Monitor)

    2002-01-01

    The Principal Component Analysis (PCA) method which we are using to fit and describe QSO spectra relies upon the fact that QSO continuum are generally very smooth and simple except for emission and absorption lines. To see this we need high signal-to-noise (S/N) spectra of QSOs at low redshift which have relatively few absorption lines in the Lyman-a forest. We need a large number of such spectra to use as the basis set for the PCA analysis which will find the set of principal component spectra which describe the QSO family as a whole. We have found that too few HST spectra have the required S/N and hence we need to supplement them with ground based spectra of QSOs at higher redshift. We have many such spectra and we have been working to make them suitable for this analysis. We have concentrated on this topic since 12/15/01.

  18. Acquired factor VIII inhibitor syndrome: A rare cause of hematuria

    PubMed Central

    Kannan, Muthuvel Seral; Raj Kumar, Thallur Ramakrishnan; Subramanian, Srinivasan

    2015-01-01

    A 50-year-old woman presented with gross hematuria for 1 month. Clinical examinations, laboratory investigations, ultrasound and contrast computed tomography were normal, except anemia. Cystoscopy revealed bloody efflux from the right side. Retrograde pyelogram showed filling defect in the renal pelvis and biopsy was inconclusive. Renal angiogram was normal. She developed ecchymosis on the right thigh and arm with elevated activated partial thromboplastin time. The partial thromboplastin time correction study and Bethesda study confirmed the presence of acquired factor VIII inhibitor (acquired hemophilia). With flexible ureterorenoscopy, the mass in the renal pelvis was removed and its histopathology revealed clotted blood. The patient was subsequently managed with steroids and Factor eight inhibitor bypass activity. PMID:25624582

  19. Potential disadvantages of using socially acquired information.

    PubMed Central

    Giraldeau, Luc-Alain; Valone, Thomas J; Templeton, Jennifer J

    2002-01-01

    The acquisition and use of socially acquired information is commonly assumed to be profitable. We challenge this assumption by exploring hypothetical scenarios where the use of such information either provides no benefit or can actually be costly. First, we show that the level of incompatibility between the acquisition of personal and socially acquired information will directly affect the extent to which the use of socially acquired information can be profitable. When these two sources of information cannot be acquired simultaneously, there may be no benefit to socially acquired information. Second, we assume that a solitary individual's behavioural decisions will be based on cues revealed by its own interactions with the environment. However, in many cases, for social animals the only socially acquired information available to individuals is the behavioural actions of others that expose their decisions, rather than the cues on which these decisions were based. We argue that in such a situation the use of socially acquired information can lead to informational cascades that sometimes result in sub-optimal behaviour. From this theory of informational cascades, we predict that when erroneous cascades are costly, individuals should pay attention only to socially generated cues and not behavioural decisions. We suggest three scenarios that might be examples of informational cascades in nature. PMID:12495513

  20. Interstellar Electron Density Spectra

    NASA Astrophysics Data System (ADS)

    Lambert, Hendrick Clark

    This study concerns the investigation of the form of the wavenumber spectrum of the Galactic electron density fluctuations through an examination of the scattering of the radio pulses emitted by pulsars as they propagate through the diffuse ionized interstellar gas. A widely used model for the electron density spectrum is based on the simple power-law: Pne(q)∝ q-β, where β = 11/3 is usually assumed, corresponding to Kolmogorov's turbulence spectrum. The simple Kolmogorov model provides satisfactory agreement for observations along many lines of sight; however, major inconsistencies remain. The inconsistencies suggest that an increase in the ratio of the power between the high (10-8[ m]-1≤ q<=10-7[ m]-1) and low (10-13[ m]-1≤ q<=10-12[ m]-1) wavenumbers is needed. This enhancement in the ratio can in turn be achieved by either including an inner scale, corresponding to a dissipation scale for the turbulent cascade, in the Kolmogorov spectrum or by considering steeper spectra. Spectra with spectral exponents β > 4 have been in general rejected based on observations of pulsar refractive scintillations. The special case of β = 4 has been given little attention and is analyzed in detail. Physically, this 'β = 4' model corresponds to the random distribution, both in location and orientation, of discrete objects with relatively sharp boundaries across the line of sight. An outer scale is included in the model to account for the average size of such objects. We compare the predictions of the inner-scale and β = 4 models both with published observations and observations we made as part of this investigation. We conclude that the form of the wavenumber spectrum is dependent on the line of sight. We propose a composite spectrum featuring a uniform background turbulence in presence of randomly distributed discrete objects, as modeled by the β = model.

  1. Automated Lipid A Structure Assignment from Hierarchical Tandem Mass Spectrometry Data

    NASA Astrophysics Data System (ADS)

    Ting, Ying S.; Shaffer, Scott A.; Jones, Jace W.; Ng, Wailap V.; Ernst, Robert K.; Goodlett, David R.

    2011-05-01

    Infusion-based electrospray ionization (ESI) coupled to multiple-stage tandem mass spectrometry (MS n ) is a standard methodology for investigating lipid A structural diversity (Shaffer et al. J. Am. Soc. Mass. Spectrom. 18(6), 1080-1092, 2007). Annotation of these MS n spectra, however, has remained a manual, expert-driven process. In order to keep up with the data acquisition rates of modern instruments, we devised a computational method to annotate lipid A MS n spectra rapidly and automatically, which we refer to as hierarchical tandem mass spectrometry (HiTMS) algorithm. As a first-pass tool, HiTMS aids expert interpretation of lipid A MS n data by providing the analyst with a set of candidate structures that may then be confirmed or rejected. HiTMS deciphers the signature ions (e.g., A-, Y-, and Z-type ions) and neutral losses of MS n spectra using a species-specific library based on general prior structural knowledge of the given lipid A species under investigation. Candidates are selected by calculating the correlation between theoretical and acquired MS n spectra. At a false discovery rate of less than 0.01, HiTMS correctly assigned 85% of the structures in a library of 133 manually annotated Francisella tularensis subspecies novicida lipid A structures. Additionally, HiTMS correctly assigned 85% of the structures in a smaller library of lipid A species from Yersinia pestis demonstrating that it may be used across species.

  2. Temporal Evolution of Solar Energetic Particle Spectra

    NASA Astrophysics Data System (ADS)

    Doran, Donald J.; Dalla, Silvia

    2016-08-01

    During solar flares and coronal mass ejections, Solar Energetic Particles (SEPs) may be released into the interplanetary medium and near-Earth locations. The energy spectra of SEP events at 1 AU are typically averaged over the entire event or studied in a few snapshots. In this article we analyze the time evolution of the energy spectra of four large selected SEP events using a large number of snapshots. We use a multi-spacecraft and multi-instrument approach for the observations, obtained over a wide SEP energy range. We find large differences in the spectra at the beginning of the events as measured by different instruments. We show that over time, a wave-like structure is observed traveling through the spectra from the highest energies to the lowest energies, creating an "arch" shape that then straightens into a power law later in the event, after times on the order of 10 hours. We discuss the processes that determine SEP intensities and their role in shaping the spectral time evolution.

  3. Acquired Brown's syndrome: an unusual cause.

    PubMed

    Booth-Mason, S; Kyle, G M; Rossor, M; Bradbury, P

    1985-10-01

    A 62-year-old man with acquired Brown's syndrome is presented. This was due to an orbital metastatic deposit, a cause not previously reported. Other causes of this disorder and its treatment are discussed.

  4. Multidimensional least-squares resolution of Raman spectra from intermediates in sensitized photochemical reactions

    SciTech Connect

    Fister, J.C. III; Harris, J.M.

    1995-12-01

    Transient resonance Raman spectroscopy is used to elicit reaction kinetics and intermediate spectra from sensitized photochemical reactions. Nonlinear least-squares analysis of Raman spectra of a triplet-state photosensitizer (benzophenone), acquired as a function of laser intensity and/or quencher concentration allow the Raman spectra of the sensitizer excited state and intermediate photoproducts to be resolved from the spectra of the ground state and solvent. In cases where physical models describing the system kinetics cannot be found, factor analysis techniques are used to obtain the intermediate spectra. Raman spectra of triplet state benzophenone and acetophenone, obtained as a function of laser excitation kinetics, and the Raman spectra of intermediates formed by energy transfer (triplet-state biacetyl) and hydrogen abstraction (benzhydrol radical) are discussed.

  5. Interpreting Chromosome Aberration Spectra

    NASA Technical Reports Server (NTRS)

    Levy, Dan; Reeder, Christopher; Loucas, Bradford; Hlatky, Lynn; Chen, Allen; Cornforth, Michael; Sachs, Rainer

    2007-01-01

    Ionizing radiation can damage cells by breaking both strands of DNA in multiple locations, essentially cutting chromosomes into pieces. The cell has enzymatic mechanisms to repair such breaks; however, these mechanisms are imperfect and, in an exchange process, may produce a large-scale rearrangement of the genome, called a chromosome aberration. Chromosome aberrations are important in killing cells, during carcinogenesis, in characterizing repair/misrepair pathways, in retrospective radiation biodosimetry, and in a number of other ways. DNA staining techniques such as mFISH ( multicolor fluorescent in situ hybridization) provide a means for analyzing aberration spectra by examining observed final patterns. Unfortunately, an mFISH observed final pattern often does not uniquely determine the underlying exchange process. Further, resolution limitations in the painting protocol sometimes lead to apparently incomplete final patterns. We here describe an algorithm for systematically finding exchange processes consistent with any observed final pattern. This algorithm uses aberration multigraphs, a mathematical formalism that links the various aspects of aberration formation. By applying a measure to the space of consistent multigraphs, we will show how to generate model-specific distributions of aberration processes from mFISH experimental data. The approach is implemented by software freely available over the internet. As a sample application, we apply these algorithms to an aberration data set, obtaining a distribution of exchange cycle sizes, which serves to measure aberration complexity. Estimating complexity, in turn, helps indicate how damaging the aberrations are and may facilitate identification of radiation type in retrospective biodosimetry.

  6. Sequencing BPS spectra

    DOE PAGES

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-03-02

    In this article, we provide both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explainmore » from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (re fined) modular S-matrix. This leads to the identi fication of modular transformations in Chern-Simons theory and 3d N = 2 theory via the 3d/3d correspondence. In conclusion, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.« less

  7. Sequencing BPS spectra

    NASA Astrophysics Data System (ADS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-03-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d {N}=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  8. USING AN ACCURATE MASS, TRIPLE QUADRUPOLE MASS SPECTROMETER AND AN ION CORRELATION PROGRAM TO IDENTIFY COMPOUNDS

    EPA Science Inventory

    Most compounds are not found in mass spectral libraries and must be identified by other means. Often, compound identities can be deduced from the compositions of the ions in their mass spectra and review of the chemical literature. Confirmation is provided by mass spectra and r...

  9. [EPR spectra of silkworm eggs].

    PubMed

    Korkhova, E D; Chepel', L M; Nikolov, O T; Komar', I N; Shakhbazov, V G

    1976-01-01

    ESR spectra of the native grain of the silkworm have been studied in the course of embryo formation, during a diapause, and during embryo development after the diapause. It is shown that the nature of ESR spectra of the grain is not determined by the metabolic processes, but by the presence of pigments in it and other stationary biological structures having developed pi-systems and unpaired electrones. The latter are mainly found in the envelope and may give the ESR spectra, with various g-factors. A dependence of the ESR spectra integral intensity of the grain on the denotype is discovered.

  10. Optimal construction of theoretical spectra for MS/MS spectra identification

    SciTech Connect

    Fridman, Tamah; Protopopescu, Vladimir A; Hurst, Gregory {Greg} B; Borziak, Andrei; Gorin, Andrey A

    2005-01-01

    We derive the optimal number of peaks (defined as the minimum number that provides the required efficiency of spectra identification) in the theoretical spectra as a function of: (i) the experimental accuracy, , of the measured ratio m/z; (ii) experimental spectrum density; (iii) size of the database; (iv) number of peaks in the theoretical spectra; and (v) types of ions that the peaks represent. We show that if theoretical spectra are constructed including b and y ions alone, then for =0.5, which is typical for high throughput data, peptide chains of 8 amino acids or longer can be identified based on the positions of peaks alone, at a rate of false identification below 1%. To discriminate between shorter peptides, additional (e.g., intensity-inferred) information is necessary. We derive the dependence of the probability of false identification on the number of peaks in the theoretical spectra and on the types of ions that the peaks represent. Our results suggest that the class of mass spectrum identification problems for which more elaborate development of fragmentation rules (such as intensity model, etc.) is required, can be reduced to the problems that involve homologous peptides.

  11. Constraining warm dark matter with cosmic shear power spectra

    SciTech Connect

    Markovic, Katarina; Weller, Jochen; Bridle, Sarah; Slosar, Anže E-mail: sarah.bridle@ucl.ac.uk E-mail: jochen.weller@usm.lmu.de

    2011-01-01

    We investigate potential constraints from cosmic shear on the dark matter particle mass, assuming all dark matter is made up of light thermal relic particles. Given the theoretical uncertainties involved in making cosmological predictions in such warm dark matter scenarios we use analytical fits to linear warm dark matter power spectra and compare (i) the halo model using a mass function evaluated from these linear power spectra and (ii) an analytical fit to the non-linear evolution of the linear power spectra. We optimistically ignore the competing effect of baryons for this work. We find approach (ii) to be conservative compared to approach (i). We evaluate cosmological constraints using these methods, marginalising over four other cosmological parameters. Using the more conservative method we find that a Euclid-like weak lensing survey together with constraints from the Planck cosmic microwave background mission primary anisotropies could achieve a lower limit on the particle mass of 2.5 keV.

  12. Development of Highly Sensitive Compact Raman Scanner for Mass Screening of Chemical Dyes

    NASA Astrophysics Data System (ADS)

    Dinish, U. S.; Fu, Chit Yaw; Olivo, Malini

    2010-08-01

    In the Raman analysis of various chemicals, it is often required to do mass screening of dyes and their derivatives. In most cases, it is impractical to screen each dye one by one on a commercial Raman system, which is catered to screen one analyte at a time. In this context, we proposed the design of simple, cost effective and compact `Raman Scanner' developed using commercial laser, detector and optical components. The high throughput screening capability of the system is demonstrated by acquiring the SERS spectra of various molecules adsorbed on to gold colloid in a 96 well plate.

  13. Micro- and nanoparticle generation during nanosecond laser ablation: correlation between mass and optical emissions.

    PubMed

    Palanco, Santiago; Marino, Salvatore; Gabás, M; Bijani, Shanti; Ayala, Luis; Ramos-Barrado, José R

    2014-02-24

    The particulate emission during nanosecond ablation of gold targets was investigated at various fluences (10-100 Jcm(-2)) and vacuum levels (0.05-750 Torr). Atomic emission spectra were acquired during the ablation process and post-mortem characterization of particle spatial distribution was performed using scanning electron microscopy. The discussion of the results in the context of existing theoretical models permitted the identification of four distinct mass removal mechanisms. While the presence, shape and intensity of atomic emission lines is a telltale of the nanoparticle formation process, the fluctuations of the emission signal over a number of laser shots was linked to the production of microscopic debris.

  14. A COMPARISON OF GADRAS SIMULATED AND MEASURED GAMMA RAY SPECTRA

    SciTech Connect

    Jeffcoat, R.; Salaymeh, S.

    2010-06-28

    Gamma-ray radiation detection systems are continuously being developed and improved for detecting the presence of radioactive material and for identifying isotopes present. Gamma-ray spectra, from many different isotopes and in different types and thicknesses of attenuation material and matrixes, are needed to evaluate the performance of these devices. Recently, a test and evaluation exercise was performed by the Savannah River National Laboratory that required a large number of gamma-ray spectra. Simulated spectra were used for a major portion of the testing in order to provide a pool of data large enough for the results to be statistically significant. The test data set was comprised of two types of data, measured and simulated. The measured data were acquired with a hand-held Radioisotope Identification Device (RIID) and simulated spectra were created using Gamma Detector Response and Analysis Software (GADRAS, Mitchell and Mattingly, Sandia National Laboratory). GADRAS uses a one-dimensional discrete ordinate calculation to simulate gamma-ray spectra. The measured and simulated spectra have been analyzed and compared. This paper will discuss the results of the comparison and offer explanations for spectral differences.

  15. Dust Spectra from Above and Below

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Spectra of martian dust taken by the Mars Exploration Rover Spirit's mini-thermal emission spectrometer are compared to that of the orbital Mars Global Surveyor's thermal emission spectrometer. The graph shows that the two instruments are in excellent agreement.

    Rover Senses Carbon Dioxide [figure removed for brevity, see original site] Click on image for larger view

    This graph, consisting of data acquired on Mars from the Mars Exploration Rover Spirit's mini-thermal emission spectrometer, shows the light, or spectral, signature of carbon dioxide. Carbon dioxide makes up the bulk of the thin martian atmosphere.

    Rover Senses Silicates [figure removed for brevity, see original site] Click on image for larger view

    This graph, consisting of data acquired on Mars by the Mars Exploration Rover Spirit's mini-thermal emission spectrometer, shows the light, or spectral, signature of silicates - a group of minerals that form the majority of Earth's crust. Minerals called feldspars and zeolites are likely candidates responsible for this feature.

    Rover Senses Bound Water [figure removed for brevity, see original site] Click on image for larger view

    This graph, consisting of data acquired on Mars from the Mars Exploration Rover Spirit's mini-thermal emission spectrometer, shows the light, or spectral, signature of an as-of-yet unidentified mineral that contains bound water in its crystal structure. Minerals such as gypsum and zeolites are possible candidates.

    Rover Senses Carbonates [figure removed for brevity, see original site] Click on image for larger view

    This graph, consisting of data from the Mars Exploration Rover Spirit's mini-thermal emission spectrometer, shows the light, or spectral, signatures of carbonates - minerals common to Earth that form only in water. The detection of trace amounts of carbonates on Mars may be due to an interaction between the water vapor in the atmosphere and minerals on the surface.

  16. HITRAN spectroscopy evaluation using solar occultation FTIR spectra

    NASA Astrophysics Data System (ADS)

    Toon, Geoffrey C.; Blavier, Jean-Francois; Sung, Keeyoon; Rothman, Laurence S.; E. Gordon, Iouli

    2016-10-01

    High resolution FTIR solar occultation spectra, acquired by the JPL MkIV Fourier transform spectrometer from balloon, covering 650-5650 cm-1 at 0.01 cm-1 resolution, are systematically analyzed using the last four versions of the HITRAN linelist (2000, 2004, 2008, 2012). The rms spectral fitting residuals are used to assess the quality and adequacy of the linelists as a function of wavenumber and altitude. Although there have been substantial overall improvements with each successive version of HITRAN, there are nevertheless a few spectral regions where the latest HITRAN version (2012) has regressed, or produces residuals that far exceed the noise level. A few of these instances are investigated further and their causes identified. We emphasize that fitting atmospheric spectra, in addition to laboratory spectra, should be part of the quality assurance for any new linelist before public release.

  17. Acquired bleeding disorders in the elderly.

    PubMed

    Kruse-Jarres, Rebecca

    2015-01-01

    The hemostatic balance changes with advancing age which may be due to factors such as platelet activation, increase of certain clotting factor proteins, slowing of the fibrinolytic system, and modification of the endothelium and blood flow. Generally, this predisposes the elderly to thrombosis rather than bleeding. It often necessitates antiplatelet or anticoagulation therapy, which can cause significant bleeding problems in an aging population. Additionally, changing renal function, modification in immune regulation, and a multitude of other disease processes, can give rise to acquired bleeding disorders. Bleeding can prove difficult to treat in a dynamic environment and in a population that may have underlying thrombotic risk factors.This article discusses some specific challenges of acquired bleeding arising in the elderly. The use of anticoagulation and nonsteroidal anti-inflammatory medications is prevalent in the treatment of the elderly and predisposes them to increased bleeding risk as their physiology changes. When prescribing and monitoring these therapies, it is exceedingly important to weigh thrombotic versus bleeding risks. There are additional rare acquired bleeding disorders that predominantly affect the elderly. One of them is acquired hemophilia, which is an autoimmune disorder arising from antibodies against factor VIII. The treatment challenge rests in the use of hemostatic agents in a population that is already at increased risk for thrombotic complications. Another rare disorder of intensifying interest, acquired von Willebrand syndrome, has a multitude of etiologic mechanisms. Understanding the underlying pathophysiology is essential in making a treatment decision for this disorder.

  18. Trion spectra of semiconductor nanostructures

    NASA Astrophysics Data System (ADS)

    Esser, Axel; Runge, Erich; Zimmermann, Roland

    2001-03-01

    The linear optical properties of quantum wells and quantum wires in the presence of a moderate background carrier density nB are investigated theoretically and compared with recent experiments. At low n_B, excitons and trions (charged excitons) are the relevant excitations. We present a density-matrix approach, which starts from the interband polarization and couples directly to higher order correlation functions which are related to three-particle excitations. It allows to describe both trionic and excitonic states. A generalized dynamical truncation scheme is applied and yields an expression for the absorption coefficient of trions in terms of trion eigenstates. Then, in combination with a numerical solution of the three-particle Schrödinger equation we sucessfully model (i) experimental photoluminescence lineshapes (their asymmetry towards lower photon energy and temperature-dependence is related to carrier recoil) [1], (ii) radiative trion lifetime (shown to depend linearly on temperature for a thermalized trion distribution) [2], and (iii) the influence of an electrical field (quantum-confined Stark effect) [3]. The optical response of excitons and trions can be studied alternatively by the solution of the time-dependent trion Schrödinger equation yielding information about (i) the appearance of trion triplet states (shown to be optically inactice at vanishing center-of-mass momentum), and (ii) exciton-electron scattering states (which give rise to a broadening of the high-energy side of the exciton). Altogether, a consistent and thorough picture of exciton related absorption spectra in the presence of additional carriers can be derived either from density matrix theory or the solution of the time-dependent three-particle Schrödinger equation. [1] A. Esser et al., Phys. Rev. B 62, 8232 (2000); [2] V. Ciulin et al., Phys. Rev. B (2000); [3] A. Esser et al., Phys. Status Solidi B 221, 281 (2000).

  19. Catalogue of representative meteor spectra

    NASA Astrophysics Data System (ADS)

    Vojáček, V.; Borovička, J.; Koten, P.; Spurný, P.; Štork, R.

    2016-01-01

    We present a library of low-resolution meteor spectra that includes sporadic meteors, members of minor meteor showers, and major meteor showers. These meteors are in the magnitude range from +2 to ‑3, corresponding to meteoroid sizes from 1 mm to10 mm. This catalogue is available online at the CDS for those interested in video meteor spectra.

  20. Projecting Spectra for Classroom Investigations.

    ERIC Educational Resources Information Center

    Sadler, Philip

    1991-01-01

    Describes an inexpensive spectrum projector that makes high-dispersion, high-efficiency diffraction gratings using a holographic process. Discusses classroom applications such as transmission spectra, absorption spectra, reflection characteristics of materials, color mixing, florescence and phosphorescence, and break up spectral colors. (MDH)

  1. Catalogue of representative meteor spectra

    NASA Astrophysics Data System (ADS)

    Vojáček, V.; Borovička, J.; Koten, P.; Spurný, P.; Štork, R.

    2016-01-01

    We present a library of low-resolution meteor spectra that includes sporadic meteors, members of minor meteor showers, and major meteor showers. These meteors are in the magnitude range from +2 to -3, corresponding to meteoroid sizes from 1 mm to10 mm. This catalogue is available online at the CDS for those interested in video meteor spectra.

  2. Cloud parallel processing of tandem mass spectrometry based proteomics data.

    PubMed

    Mohammed, Yassene; Mostovenko, Ekaterina; Henneman, Alex A; Marissen, Rob J; Deelder, André M; Palmblad, Magnus

    2012-10-01

    Data analysis in mass spectrometry based proteomics struggles to keep pace with the advances in instrumentation and the increasing rate of data acquisition. Analyzing this data involves multiple steps requiring diverse software, using different algorithms and data formats. Speed and performance of the mass spectral search engines are continuously improving, although not necessarily as needed to face the challenges of acquired big data. Improving and parallelizing the search algorithms is one possibility; data decomposition presents another, simpler strategy for introducing parallelism. We describe a general method for parallelizing identification of tandem mass spectra using data decomposition that keeps the search engine intact and wraps the parallelization around it. We introduce two algorithms for decomposing mzXML files and recomposing resulting pepXML files. This makes the approach applicable to different search engines, including those relying on sequence databases and those searching spectral libraries. We use cloud computing to deliver the computational power and scientific workflow engines to interface and automate the different processing steps. We show how to leverage these technologies to achieve faster data analysis in proteomics and present three scientific workflows for parallel database as well as spectral library search using our data decomposition programs, X!Tandem and SpectraST.

  3. High precision radial velocities with GIANO spectra

    NASA Astrophysics Data System (ADS)

    Carleo, I.; Sanna, N.; Gratton, R.; Benatti, S.; Bonavita, M.; Oliva, E.; Origlia, L.; Desidera, S.; Claudi, R.; Sissa, E.

    2016-06-01

    Radial velocities (RV) measured from near-infrared (NIR) spectra are a potentially excellent tool to search for extrasolar planets around cool or active stars. High resolution infrared (IR) spectrographs now available are reaching the high precision of visible instruments, with a constant improvement over time. GIANO is an infrared echelle spectrograph at the Telescopio Nazionale Galileo (TNG) and it is a powerful tool to provide high resolution spectra for accurate RV measurements of exoplanets and for chemical and dynamical studies of stellar or extragalactic objects. No other high spectral resolution IR instrument has GIANO's capability to cover the entire NIR wavelength range (0.95-2.45 μm) in a single exposure. In this paper we describe the ensemble of procedures that we have developed to measure high precision RVs on GIANO spectra acquired during the Science Verification (SV) run, using the telluric lines as wavelength reference. We used the Cross Correlation Function (CCF) method to determine the velocity for both the star and the telluric lines. For this purpose, we constructed two suitable digital masks that include about 2000 stellar lines, and a similar number of telluric lines. The method is applied to various targets with different spectral type, from K2V to M8 stars. We reached different precisions mainly depending on the H-magnitudes: for H ˜ 5 we obtain an rms scatter of ˜ 10 m s-1, while for H ˜ 9 the standard deviation increases to ˜ 50 ÷ 80 m s-1. The corresponding theoretical error expectations are ˜ 4 m s-1 and 30 m s-1, respectively. Finally we provide the RVs measured with our procedure for the targets observed during GIANO Science Verification.

  4. Beamstrahlung spectra in next generation linear colliders

    SciTech Connect

    Barklow, T.; Chen, P. ); Kozanecki, W. )

    1992-04-01

    For the next generation of linear colliders, the energy loss due to beamstrahlung during the collision of the e{sup +}e{sup {minus}} beams is expected to substantially influence the effective center-of-mass energy distribution of the colliding particles. In this paper, we first derive analytical formulae for the electron and photon energy spectra under multiple beamstrahlung processes, and for the e{sup +}e{sup {minus}} and {gamma}{gamma} differential luminosities. We then apply our formulation to various classes of 500 GeV e{sup +}e{sup {minus}} linear collider designs currently under study.

  5. Differential Protein Expression in Congenital and Acquired Cholesteatomas

    PubMed Central

    Kim, Sung Huhn; Choi, Jae Young

    2015-01-01

    Congenital cholesteatomas are epithelial lesions that present as an epithelial pearl behind an intact eardrum. Congenital and acquired cholesteatomas progress quite differently from each other and progress patterns can provide clues about the unique origin and pathogenesis of the abnormality. However, the exact pathogenic mechanisms by which cholesteatomas develop remain unknown. In this study, key proteins that directly affect cholesteatoma pathogenesis are investigated with proteomics and immunohistochemistry. Congenital cholesteatoma matrices and retroauricular skin were harvested during surgery in 4 patients diagnosed with a congenital cholesteatoma. Tissue was also harvested from the retraction pocket in an additional 2 patients during middle ear surgery. We performed 2-dimensional (2D) electrophoresis to detect and analyze spots that are expressed only in congenital cholesteatoma and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) to separate proteins by molecular weight. Protein expression was confirmed by immunohistochemical staining. The image analysis of 2D electrophoresis showed that 4 congenital cholesteatoma samples had very similar protein expression patterns and that 127 spots were exclusively expressed in congenital cholesteatomas. Of these 127 spots, 10 major spots revealed the presence of titin, forkhead transcription activator homolog (FKH 5–3), plectin 1, keratin 10, and leucine zipper protein 5 by MALDI-TOF/MS analysis. Immunohistochemical staining showed that FKH 5–3 and titin were expressed in congenital cholesteatoma matrices, but not in acquired cholesteatomas. Our study shows that protein expression patterns are completely different in congenital cholesteatomas, acquired cholesteatomas, and skin. Moreover, non-epithelial proteins, including FKH 5–3 and titin, were unexpectedly expressed in congenital cholesteatoma tissue. Our data indicates that congenital cholesteatoma origins may differ

  6. Acquired cutis laxa associated with cutaneous mastocytosis.

    PubMed

    Hoang, Minh Van; Dang, Phuoc Van; Bui, Duc Van; Mejbel, Haider; Mani, Divya Thomas; Smoller, Bruce Robert; Phung, Thuy Linh

    2015-07-01

    Cutis laxa is characterized by dramatic wrinkling of skin that is lacking in elasticity due to inherent defects in dermal elastic fibers. Cutis laxa can be caused by genetic and metabolic disorders. It can also be acquired, possibly resulting from inflammatory processes with destruction of elastic fibers. This report describes a 26-year old woman who developed acquired cutis laxa and cutaneous mastocytosis leading to premature aging. She represents a unique co-occurrence of these two separate disease entities. To our knowledge, there has been only one published case report of acquired cutis laxa occurring in association with urticaria pigmentosa in a 4-year old girl. Our case would be a second case that exhibits the coexistence of these two disorders in an adult female. PMID:26436968

  7. Properties of Martian Hematite at Meridiani Planum by Simultaneous Fitting of Mars Mossbauer Spectra

    NASA Technical Reports Server (NTRS)

    Agresti, D. G.; Fleischer, I.; Klingelhoefer, G.; Morris, R. V.

    2010-01-01

    Mossbauer spectrometers [1] on the two Mars Exploration Rovers (MERs) have been making measurements of surface rocks and soils since January 2004, recording spectra in 10-K-wide temperature bins ranging from 180 K to 290 K. Initial analyses focused on modeling individual spectra directly as acquired or, to increase statistical quality, as sums of single-rock or soil spectra over temperature or as sums over similar rock or soil type [2, 3]. Recently, we have begun to apply simultaneous fitting procedures [4] to Mars Mossbauer data [5-7]. During simultaneous fitting (simfitting), many spectra are modeled similarly and fit together to a single convergence criterion. A satisfactory simfit with parameter values consistent among all spectra is more likely than many single-spectrum fits of the same data because fitting parameters are shared among multiple spectra in the simfit. Consequently, the number of variable parameters, as well as the correlations among them, is greatly reduced. Here we focus on applications of simfitting to interpret the hematite signature in Moessbauer spectra acquired at Meridiani Planum, results of which were reported in [7]. The Spectra. We simfit two sets of spectra with large hematite content [7]: 1) 60 rock outcrop spectra from Eagle Crater; and 2) 46 spectra of spherule-rich lag deposits (Table 1). Spectra of 10 different targets acquired at several distinct temperatures are included in each simfit set. In the table, each Sol (martian day) represents a different target, NS is the number of spectra for a given sol, and NT is the number of spectra for a given temperature. The spectra are indexed to facilitate definition of parameter relations and constraints. An example spectrum is shown in Figure 1, together with a typical fitting model. Results. We have shown that simultaneous fitting is effective in analyzing a large set of related MER Mossbauer spectra. By using appropriate constraints, we derive target-specific quantities and the

  8. Congenital and acquired bleeding disorders in infancy.

    PubMed

    Campbell, Sally Elizabeth; Bolton-Maggs, Paula H B

    2015-11-01

    The diagnosis of congenital and acquired bleeding disorders in infants requires an understanding of developmental haemostasis and the effect on laboratory testing. A systematic approach to bleeding in neonates will aid clinicians in the diagnosis and treatment, which may be caused by a wide variety of diseases. The clinical setting will help to direct the diagnostic pathway. This review will focus on the presentation and diagnosis of congenital and acquired bleeding disorders, including platelet disorders. Current research in this field is ongoing, including investigation into neonatal platelets and their different functionalities, platelet transfusion thresholds and how changes in coagulation factors may be linked to other homeostatic mechanisms.

  9. Evolution and infrared spectra of brown dwarfs

    NASA Technical Reports Server (NTRS)

    Lunine, Jonathan I.; Hubbard, William B.; Marley, Mark S.

    1986-01-01

    Self-consistent models are constructed for the structure, evolution, and observable properties of degenerately cooling objects, or 'brown dwarfs'. Model atmospheres composed of a range of likely gaseous and particulate opacity sources are calculated in order to provide a boundary condition for interior temperature-pressure profiles and to determine the emergent spectra for such objects. The radius derived from the interior models is combined with the emergent fluxes calculated from the atmosphere model to fit the data of McCarthy, Probst, and Low (1985) and to derive the luminosity and mass of VB 8B. The latter is found to be most probably an 0.05 solar mass object with effective temperature in the 1200-1500 K range and an atmosphere which very likely contains particulate absorbers. Key changes in chemical oxidation state and condensation of major constituents during the evolution of brown dwarfs are presented.

  10. A Case Of Bilateral Acquired Localized Lipoatrophy

    PubMed Central

    Tanrıkulu, Osman; Yesilova, Yavuz; Aksoy, Mustafa

    2016-01-01

    Lipoatrophy is characterized by inflammation and tissue loss in fatty tissue. This disease may be congenital or acquired, primary or secondary. Secondary lipoatrophy develops with infections, collagen tissue diseases, tumors and drug injections. In this report, we present the case of a 14-year-old female patient who developed lipoatrophy following intramuscular steroid injection to both buttocks. PMID:27504088

  11. Mitral valve repair in acquired dextrocardia.

    PubMed

    Elmistekawy, Elsayed; Chan, Vincent; Hynes, Mark; Mesana, Thierry

    2015-10-01

    Surgical correction of valvular heart disease in patients with dextrocardia is extremely rare. We report a surgical case of mitral valve repair in a patient with acquired dextrocardia. Successful mitral valve repair was performed through a right lateral thoracotomy. We describe our surgical strategy and summarize the literature.

  12. Acquired immunodeficiency syndrome with subacute sclerosing panencephalitis.

    PubMed

    Gowda, Vykuntaraju K N; Sukanya, V; Shivananda

    2012-11-01

    A 7-year-old boy with acquired immunodeficiency syndrome, receiving antiretroviral drugs for 2 years, presented with a recent onset of myoclonic jerks and cognitive deterioration. On examination, he manifested myoclonic jerks once every 10-15 seconds. His electroencephalogram indicated periodic complexes, and his cerebrospinal fluid tested positive for measles antibodies.

  13. How Did Light Acquire a Velocity?

    ERIC Educational Resources Information Center

    Lauginie, Pierre

    2013-01-01

    We discuss how light acquired a velocity through history, from the ancient Greeks to the early modern era. Combining abstract debates, models of light, practical needs, planned research and chance, this history illustrates several key points that should be brought out in science education.

  14. Group Treatment in Acquired Brain Injury Rehabilitation

    ERIC Educational Resources Information Center

    Bertisch, Hilary; Rath, Joseph F.; Langenbahn, Donna M.; Sherr, Rose Lynn; Diller, Leonard

    2011-01-01

    The current article describes critical issues in adapting traditional group-treatment methods for working with individuals with reduced cognitive capacity secondary to acquired brain injury. Using the classification system based on functional ability developed at the NYU Rusk Institute of Rehabilitation Medicine (RIRM), we delineate the cognitive…

  15. Support Network Responses to Acquired Brain Injury

    ERIC Educational Resources Information Center

    Chleboun, Steffany; Hux, Karen

    2011-01-01

    Acquired brain injury (ABI) affects social relationships; however, the ways social and support networks change and evolve as a result of brain injury is not well understood. This study explored ways in which survivors of ABI and members of their support networks perceive relationship changes as recovery extends into the long-term stage. Two…

  16. Interviewing Children with Acquired Brain Injury (ABI)

    ERIC Educational Resources Information Center

    Boylan, Anne-Marie; Linden, Mark; Alderdice, Fiona

    2009-01-01

    Research into the lives of children with acquired brain injury (ABI) often neglects to incorporate children as participants, preferring to obtain the opinions of the adult carer (e.g. McKinlay et al., 2002). There has been a concerted attempt to move away from this position by those working in children's research with current etiquette…

  17. Eye Movement Correlates of Acquired Central Dyslexia

    ERIC Educational Resources Information Center

    Schattka, Kerstin I.; Radach, Ralph; Huber, Walter

    2010-01-01

    Based on recent progress in theory and measurement techniques, the analysis of eye movements has become one of the major methodological tools in experimental reading research. Our work uses this approach to advance the understanding of impaired information processing in acquired central dyslexia of stroke patients with aphasia. Up to now there has…

  18. 7 CFR 989.17 - Acquire.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 8 2013-01-01 2013-01-01 false Acquire. 989.17 Section 989.17 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (MARKETING AGREEMENTS AND ORDERS; FRUITS, VEGETABLES, NUTS), DEPARTMENT OF AGRICULTURE RAISINS PRODUCED FROM GRAPES GROWN...

  19. 7 CFR 989.17 - Acquire.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Acquire. 989.17 Section 989.17 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements and Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE RAISINS PRODUCED FROM GRAPES GROWN...

  20. 7 CFR 989.17 - Acquire.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 8 2014-01-01 2014-01-01 false Acquire. 989.17 Section 989.17 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (MARKETING AGREEMENTS AND ORDERS; FRUITS, VEGETABLES, NUTS), DEPARTMENT OF AGRICULTURE RAISINS PRODUCED FROM GRAPES GROWN...

  1. 7 CFR 989.17 - Acquire.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 8 2011-01-01 2011-01-01 false Acquire. 989.17 Section 989.17 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements and Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE RAISINS PRODUCED FROM GRAPES GROWN...

  2. Neural Correlates of Acquired Color Category Effects

    ERIC Educational Resources Information Center

    Clifford, Alexandra; Franklin, Anna; Holmes, Amanda; Drivonikou, Vicky G.; Ozgen, Emre; Davies, Ian R. L.

    2012-01-01

    Category training can induce category effects, whereby color discrimination of stimuli spanning a newly learned category boundary is enhanced relative to equivalently spaced stimuli from within the newly learned category (e.g., categorical perception). However, the underlying mechanisms of these acquired category effects are not fully understood.…

  3. Nonlinear matter spectra in growing neutrino quintessence

    SciTech Connect

    Brouzakis, N.; Tetradis, N.; Pettorino, V.; Wetterich, C. E-mail: pettorin@sissa.it E-mail: c.wetterich@thphys.uni-heidelberg.de

    2011-03-01

    We investigate the nonlinear power spectra of density perturbations and acoustic oscillations in growing neutrino quintessence. In this scenario, the neutrino mass has a strong dependence on the quintessence field. The induced coupling stops the evolution of the field when the neutrinos become nonrelativistic, and triggers the transition to the accelerating phase of the cosmological expansion. For the calculation of the nonlinear spectra we employ the time renormalization group, which resums subsets of diagrams of arbitrarily high order in cosmological perturbation theory. At redshifts around five, the neutrino fluctuations are still linear and acoustic oscillations are present in the neutrino power spectrum, induced by the acoustic oscillations in the baryonic and dark-matter sectors. The neutrino perturbations become nonlinear at redshifts around three. The mode coupling generated by the nonlinearities erases the oscillations in the neutrino spectrum at some redshift above two. There is a potential danger that at later times the influence of the gravitational potentials induced by the neutrino inhomogeneities could erase the oscillations from the baryonic and dark-matter spectra, making the scenario incompatible with observations. For the scenario to be viable, the neutrino-induced gravitational potentials in the range of baryon acoustic oscillations should not grow to average values much larger than 10{sup −4}. The magnitude of the expected potentials is still not known reliably, as the process of structure formation is poorly understood in growing neutrino quintessence. The time renormalization group cannot describe the effects of nonlinear clustering. Alternative methods, such as hydrodynamic simulations, must be empoloyed for the calculation of the spectra at low redshifts.

  4. [Instantaneous emission spectra of epoxypropane in the process of deflagration to detonation transition].

    PubMed

    Li, Ping; Yuan, Chang-ying; Hu, Dong; Liu, Jun-chao; Zhu-mei, Sun; Dong, Shi; Xiao, Hai-bo

    2004-07-01

    Using an intensified CCD spectroscopic detector (Princeton Instruments, ICCD PI-Max 1024 RB) which can be gated in as little as 5 ns, the synchronization of the measuring system was controlled by a digital delay generator (Stanford Research Systems, DG535), the DG535 was triggered externally by a lab-made electrical pulse generator which transformed the optical trigger signal to an electrical signal, and the light signal from the end window of an explosion shock tube was delivered by an 1 mm in diameter plastic optical fiber to the entrance slit of the spectrometer (grating of 150 g x mm(-1) , central wavelength of 550 nm). The spectrum measurement of the epoxypropane in the process of deflagration to detonation transition (DDT) was then made. The instantaneous emission spectra of epoxypropane at different time of the DDT process with an exposure time of several microseconds were acquired. Results show that at the beginning of the DDT process, the emitted light was very weak and the line spectra of atoms were observed mainly; in the middle process of the DDT, the emitted light became strong and the spectra observed consisted of line spectra of atoms, band spectra of molecules plus continuous spectrum of the thermal radiation; when the detonation was formed, the emitted light got very strong, and the spectra acquired consisted of both line spectra of atoms and band spectra of molecules superimposed on the strong continuum of the thermal radiation. PMID:15766070

  5. [Instantaneous emission spectra of epoxypropane in the process of deflagration to detonation transition].

    PubMed

    Li, Ping; Yuan, Chang-ying; Hu, Dong; Liu, Jun-chao; Zhu-mei, Sun; Dong, Shi; Xiao, Hai-bo

    2004-07-01

    Using an intensified CCD spectroscopic detector (Princeton Instruments, ICCD PI-Max 1024 RB) which can be gated in as little as 5 ns, the synchronization of the measuring system was controlled by a digital delay generator (Stanford Research Systems, DG535), the DG535 was triggered externally by a lab-made electrical pulse generator which transformed the optical trigger signal to an electrical signal, and the light signal from the end window of an explosion shock tube was delivered by an 1 mm in diameter plastic optical fiber to the entrance slit of the spectrometer (grating of 150 g x mm(-1) , central wavelength of 550 nm). The spectrum measurement of the epoxypropane in the process of deflagration to detonation transition (DDT) was then made. The instantaneous emission spectra of epoxypropane at different time of the DDT process with an exposure time of several microseconds were acquired. Results show that at the beginning of the DDT process, the emitted light was very weak and the line spectra of atoms were observed mainly; in the middle process of the DDT, the emitted light became strong and the spectra observed consisted of line spectra of atoms, band spectra of molecules plus continuous spectrum of the thermal radiation; when the detonation was formed, the emitted light got very strong, and the spectra acquired consisted of both line spectra of atoms and band spectra of molecules superimposed on the strong continuum of the thermal radiation.

  6. Visible and Near-IR Reflectance Spectra of Mars Analogue Materials Under Arid Conditions for Interpretation of Martian Surface Mineralogy

    NASA Technical Reports Server (NTRS)

    Morris, R. V.; Graff, T. G.; Achilles, C. N.; Agresti, D. G.; Ming, D. W.; Golden, D. C.

    2011-01-01

    Visible and near-IR (VNIR) spectra from the hyper-spectral imagers MRO-CRISM and Mars Express OMEGA in martian orbit have signatures from Fe-bearing phases (e.g., olivine, pyroxene, and jarosite), H2O/OH-bearing phases (e.g., smectites and other phyllosilicates, sulfates, and high-SiO2 phases), and carbonate [e.g., 1-5]. Mineralogical assignments of martian spectral features are made on the basis of VNIR spectra acquired in the laboratory under appropriate environmental conditions on samples whose mineralogical composition is known. We report here additional results for our ongoing project [6] to acquire VNIR spectra under arid conditions.

  7. Space Telescope Imaging Spectrograph Ultraviolet Spectra of Large Magellanic Cloud Planetary Nebulae: A Study of Carbon Abundances and Stellar Evolution

    NASA Astrophysics Data System (ADS)

    Stanghellini, Letizia; Shaw, Richard A.; Gilmore, Diane

    2005-03-01

    We acquired spectra of 24 LMC planetary nebulae (PNs) in the 1150-3000 Å range in order to determine carbon and other ionic abundances. The sample more than doubles the number of LMC PNs with high-quality UV spectra in this wavelength range and whose optical images are available in the Hubble Space Telescope archive. The Space Telescope Imaging Spectrograph was used with a very large aperture to obtain virtually slitless spectra; thus, the monochromatic images in the major nebula emission lines are also available. The analysis of the data shows extremely high quality spectra. This paper presents the emission lines identified and measured and the calculation of the ionic abundances of the emitting carbon and other ions, as well as total carbon abundance. P Cygni profiles have been found in a fraction of the nebulae, and the limiting velocities of the stellar winds estimated. The total carbon abundance can be inferred reliably in most nebulae. We found that the average carbon abundance in round and elliptical PNs is one order of magnitude larger than that of the bipolar PNs, while elliptical and round PNs with a bipolar core have a bimodal behavior. This results confirm that bipolarity in LMC PNs is tightly correlated with high-mass progenitors. When compared with predicted yields, we found that the observed abundance ratio shows a shift toward higher carbon abundances, which may be due to initial conditions assumed in the models not appropriate for LMC PNs. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.

  8. Lunar orbital mass spectrometer experiment

    NASA Technical Reports Server (NTRS)

    Lord, W. P.

    1971-01-01

    The design, development, manufacture, test and calibration of five lunar orbital mass spectrometers with the four associated ground support equipment test sets are discussed. A mass spectrometer was installed in the Apollo 15 and one in the Apollo 16 Scientific Instrument Module within the Service Module. The Apollo 15 mass spectrometer was operated with collection of 38 hours of mass spectra data during lunar orbit and 50 hours of data were collected during transearth coast. The Apollo 16 mass spectrometer was operated with collection of 76 hours of mass spectra data during lunar orbit. However, the Apollo 16 mass spectrometer was ejected into lunar orbit upon malfunction of spacecraft boom system just prior to transearth insection and no transearth coast data was possible.

  9. Depth profiling code for analyzing ERD-TOF spectra

    NASA Astrophysics Data System (ADS)

    Mathot, G.; Terwagne, G.; Bodart, F.

    2001-07-01

    A computer program calculating depth profiles of light elements in surface layer of various materials from experimental ERD-TOF spectra has been developed. The program, which is able to identify the recoil particles, makes multi-element profiling by sorting the spectra by mass. The interactive spectrum synthesis compare the real recoils spectra with simulated spectra of the assumed target. The program is also able to calculate the atomic concentration ratios without any a priori assumption of the composition of an unknown target. The stopping power used in the analysis package respect the Alegria [1] format and can be easily upgraded and modified by the user. It can be calculated for any particle target combination and beam energy between 100 keV and 15 MeV. The calculation takes also into account for the straggling, the energy loss in the carbon foils of the start and the stop detectors and the entry window of the particle detector.

  10. XMS: Cross-Platform Normalization Method for Multimodal Mass Spectrometric Tissue Profiling

    NASA Astrophysics Data System (ADS)

    Golf, Ottmar; Muirhead, Laura J.; Speller, Abigail; Balog, Júlia; Abbassi-Ghadi, Nima; Kumar, Sacheen; Mróz, Anna; Veselkov, Kirill; Takáts, Zoltán

    2015-01-01

    Here we present a proof of concept cross-platform normalization approach to convert raw mass spectra acquired by distinct desorption ionization methods and/or instrumental setups to cross-platform normalized analyte profiles. The initial step of the workflow is database driven peak annotation followed by summarization of peak intensities of different ions from the same molecule. The resulting compound-intensity spectra are adjusted to a method-independent intensity scale by using predetermined, compound-specific normalization factors. The method is based on the assumption that distinct MS-based platforms capture a similar set of chemical species in a biological sample, though these species may exhibit platform-specific molecular ion intensity distribution patterns. The method was validated on two sample sets of (1) porcine tissue analyzed by laser desorption ionization (LDI), desorption electrospray ionization (DESI), and rapid evaporative ionization mass spectrometric (REIMS) in combination with Fourier transformation-based mass spectrometry; and (2) healthy/cancerous colorectal tissue analyzed by DESI and REIMS with the latter being combined with time-of-flight mass spectrometry. We demonstrate the capacity of our method to reduce MS-platform specific variation resulting in (1) high inter-platform concordance coefficients of analyte intensities; (2) clear principal component based clustering of analyte profiles according to histological tissue types, irrespective of the used desorption ionization technique or mass spectrometer; and (3) accurate "blind" classification of histologic tissue types using cross-platform normalized analyte profiles.

  11. Storage and retrieval of mass spectral information

    NASA Technical Reports Server (NTRS)

    Hohn, M. E.; Humberston, M. J.; Eglinton, G.

    1977-01-01

    Computer handling of mass spectra serves two main purposes: the interpretation of the occasional, problematic mass spectrum, and the identification of the large number of spectra generated in the gas-chromatographic-mass spectrometric (GC-MS) analysis of complex natural and synthetic mixtures. Methods available fall into the three categories of library search, artificial intelligence, and learning machine. Optional procedures for coding, abbreviating and filtering a library of spectra minimize time and storage requirements. Newer techniques make increasing use of probability and information theory in accessing files of mass spectral information.

  12. Predicting charmonium and bottomonium spectra with a quark harmonic oscillator.

    PubMed

    Norbury, J W; Badavi, F F; Townsend, L W

    1986-11-01

    We present a simple application of the three-dimensional harmonic oscillator which should provide a very nice particle physics example to be presented in introductory undergraduate quantum mechanics course. The idea is to use the nonrelativistic quark model to calculate the spin-averaged mass levels of the charmonium and bottomonium spectra. PMID:11538828

  13. Acquired undescended testis: putting the pieces together.

    PubMed

    Hack, W W M; Goede, J; van der Voort-Doedens, L M; Meijer, R W

    2012-02-01

    Acquired undescended testis is now a well-recognized disorder. It is seen in 1.5% of pre-pubertal boys and accounts for the 1-2% orchidopexy rate in older boys. Its pathogenesis remains largely unclear, but it may be caused by a fibrous remnant of the processus vaginalis. There is much controversy over its management, and the proper management awaits a randomized-controlled trial. Until now, follow-up data are available only for cases of spontaneous descent or pubertal orchidopexy. It is speculated that acquired undescended testis is in fact congenital and because of a short funiculus at birth, allowing a low-scrotal position early in life. However, as the boy grows, the testis might evolve into an undescended state. When testosterone surges at puberty, spontaneous descent occurs in three of every four cases.

  14. Clinical laboratory data: acquire, analyze, communicate, liberate.

    PubMed

    Azzazy, Hassan M E; Elbehery, Ali H A

    2015-01-01

    The availability of portable healthcare devices, which can acquire and transmit medical data to remote experts would dramatically affect healthcare in areas with poor infrastructure. Smartphones, which feature touchscreen computer capabilities and sophisticated cameras, have become widely available with over billion units shipped in 2013. In the clinical laboratory, smartphones have recently brought the capabilities of key instruments such as spectrophotometers, fluorescence analyzers and microscopes into the palm of the hand. Several research groups have developed sensitive and low-cost smartphone-based diagnostic assay prototypes for testing cholesterol, albumin, vitamin D, tumor markers, and the detection of infectious agents. This review covers the use of smartphones to acquire, analyze, communicate, and liberate clinical laboratory data. Smartphones promise to dramatically improve the quality and quantity of healthcare offered in resource-limited areas.

  15. Acquired Cystic Fibrosis Transmembrane Conductance Regulator Deficiency.

    PubMed

    Cho, Do-Yeon; Woodworth, Bradford A

    2016-01-01

    In the genetic airway disease cystic fibrosis (CF), deficiency or dysfunction of the cystic fibrosis membrane conductance regulator (CFTR) alters anion transport in respiratory epithelium and consequently disrupts mucociliary clearance. An enriched understanding of the role of CFTR in the maintenance of normal epithelial function has revealed that mild and variable CFTR mutations play a causative role in a number of diseases not classically associated with CF. Furthermore, recent evidence indicates that acquired defects in wild-type CFTR protein processing, endocytic recycling and function can contribute to the pathogenesis of airway diseases, such as chronic obstructive pulmonary disease. In this chapter, we discuss emerging findings implicating acquired CFTR dysfunction in the pathogenesis of chronic rhinosinusitis and propose a new and leading edge approach to future CRS therapy using CFTR potentiators. PMID:27466849

  16. Acquired portosystemic collaterals: anatomy and imaging*

    PubMed Central

    Leite, Andréa Farias de Melo; Mota Jr., Américo; Chagas-Neto, Francisco Abaeté; Teixeira, Sara Reis; Elias Junior, Jorge; Muglia, Valdair Francisco

    2016-01-01

    Portosystemic shunts are enlarged vessels that form collateral pathological pathways between the splanchnic circulation and the systemic circulation. Although their causes are multifactorial, portosystemic shunts all have one mechanism in common-increased portal venous pressure, which diverts the blood flow from the gastrointestinal tract to the systemic circulation. Congenital and acquired collateral pathways have both been described in the literature. The aim of this pictorial essay was to discuss the distinct anatomic and imaging features of portosystemic shunts, as well as to provide a robust method of differentiating between acquired portosystemic shunts and similar pathologies, through the use of illustrations and schematic drawings. Imaging of portosystemic shunts provides subclinical markers of increased portal venous pressure. Therefore, radiologists play a crucial role in the identification of portosystemic shunts. Early detection of portosystemic shunts can allow ample time to perform endovascular shunt operations, which can relieve portal hypertension and prevent acute or chronic complications in at-risk patient populations. PMID:27777479

  17. [Acquired renal cysts in maintenance dialysis patients].

    PubMed

    Lie, B; Hust, W; Asgarzadeh, A; Mann, H

    1986-03-01

    Ultrasonographic examination of the kidneys of 111 patients on long term maintenance hemodialysis was performed. None of the patients had genuine polycystic kidney disease. In many patients acquired cysts were found. Frequency and volume of these cysts were the same on the right and left side. There was no correlation between the age of the patients and the number of cysts. There were no differences concerning sex and type of primary renal disease. There was a significant positive correlation between time on maintenance hemodialysis and number of cysts but no correlation between number of cysts and hemoglobin concentration. This is in contrast to data in the literature. Clinical relevance of acquired kidney cysts in dialysis patients concerns hematuria, retroperitoneal bleeding, kidney stone formation, septicemia and malignancy.

  18. Acquired Muscle Weakness in the Surgical Intensive Care Unit: Nosology, Epidemiology, Diagnosis, and Prevention.

    PubMed

    Farhan, Hassan; Moreno-Duarte, Ingrid; Latronico, Nicola; Zafonte, Ross; Eikermann, Matthias

    2016-01-01

    Muscle weakness is common in the surgical intensive care unit (ICU). Low muscle mass at ICU admission is a significant predictor of adverse outcomes. The consequences of ICU-acquired muscle weakness depend on the underlying mechanism. Temporary drug-induced weakness when properly managed may not affect outcome. Severe perioperative acquired weakness that is associated with adverse outcomes (prolonged mechanical ventilation, increases in ICU length of stay, and mortality) occurs with persistent (time frame: days) activation of protein degradation pathways, decreases in the drive to the skeletal muscle, and impaired muscular homeostasis. ICU-acquired muscle weakness can be prevented by early treatment of the underlying disease, goal-directed therapy, restrictive use of immobilizing medications, optimal nutrition, activating ventilatory modes, early rehabilitation, and preventive drug therapy. In this article, the authors review the nosology, epidemiology, diagnosis, and prevention of ICU-acquired weakness in surgical ICU patients. PMID:26445385

  19. Acquired Muscle Weakness in the Surgical Intensive Care Unit: Nosology, Epidemiology, Diagnosis, and Prevention.

    PubMed

    Farhan, Hassan; Moreno-Duarte, Ingrid; Latronico, Nicola; Zafonte, Ross; Eikermann, Matthias

    2016-01-01

    Muscle weakness is common in the surgical intensive care unit (ICU). Low muscle mass at ICU admission is a significant predictor of adverse outcomes. The consequences of ICU-acquired muscle weakness depend on the underlying mechanism. Temporary drug-induced weakness when properly managed may not affect outcome. Severe perioperative acquired weakness that is associated with adverse outcomes (prolonged mechanical ventilation, increases in ICU length of stay, and mortality) occurs with persistent (time frame: days) activation of protein degradation pathways, decreases in the drive to the skeletal muscle, and impaired muscular homeostasis. ICU-acquired muscle weakness can be prevented by early treatment of the underlying disease, goal-directed therapy, restrictive use of immobilizing medications, optimal nutrition, activating ventilatory modes, early rehabilitation, and preventive drug therapy. In this article, the authors review the nosology, epidemiology, diagnosis, and prevention of ICU-acquired weakness in surgical ICU patients.

  20. System Acquires Data On Reactivities Of Foams

    NASA Technical Reports Server (NTRS)

    Walls, Joe T.

    1994-01-01

    Data-acquisition and -plotting system, called DAPS(TM), developed enabling accurate and objective determination of physical properties related to reactivities of polyurethane and polyisocyanurate foams. Automated, computer-controlled test apparatus that acquires data on rates of rise, rise profiles, exothermic temperatures, and internal pressures of foams prepared from both manual and machine-mixed batches. Data used to determine minute differences between reaction kinetics and exothermic profiles of foam formulations, properties of end products which are statistically undifferentiated.

  1. Management options of acquired punctal stenosis.

    PubMed

    Bukhari, Amal A

    2013-08-01

    Punctal stenosis is a frequent source of patients referral to the otoplasty clinic and the search for a procedure that can permanently eliminate epiphora without disturbing the normal lacrimal system anatomy and physiology started centuries ago and continues today. The following article summarizes the reported procedures in the English literature in the acquired punctal stenosis with a description of techniques, success rates, and potential complications with the goal of identifying the most effective treatment strategy based on the current knowledge available.

  2. Earth Knowledge Acquired by Middle School Students

    NASA Technical Reports Server (NTRS)

    Ride, Sally

    2008-01-01

    Earth Knowledge Acquired by Middle School Students (EarthKAM), an education activity, allows middle school students to program a digital camera on board the International Space Station to photograph a variety of geographical targets for study in the classroom. Photos are made available on the web for viewing and study by participating schools around the world. Educators use the images for projects involving Earth Science, geography, physics, and social science.

  3. Acquired protein energy malnutrition in glutaric acidemia.

    PubMed

    Ma, Liqiao; Savory, Stephanie; Agim, Nnenna G

    2013-01-01

    We report a case of acquired protein energy malnutrition with associated zinc deficiency in an 18-month-old boy with type 1 glutaric acidemia. Physical examination findings included generalized nonpitting edema, widespread desquamative plaques, and sparse hair with a reddish tinge. Laboratory abnormalities included low levels of zinc, albumin, alkaline phosphatase, and iron. A review of skin manifestations of nutritional deficiencies, specifically kwashiorkor, is presented, as well as the relatively new entity called acrodermatitis dysmetabolica.

  4. Acquired protein energy malnutrition in glutaric acidemia.

    PubMed

    Ma, Liqiao; Savory, Stephanie; Agim, Nnenna G

    2013-01-01

    We report a case of acquired protein energy malnutrition with associated zinc deficiency in an 18-month-old boy with type 1 glutaric acidemia. Physical examination findings included generalized nonpitting edema, widespread desquamative plaques, and sparse hair with a reddish tinge. Laboratory abnormalities included low levels of zinc, albumin, alkaline phosphatase, and iron. A review of skin manifestations of nutritional deficiencies, specifically kwashiorkor, is presented, as well as the relatively new entity called acrodermatitis dysmetabolica. PMID:23330977

  5. Acquired Antibiotic Resistance Genes: An Overview

    PubMed Central

    van Hoek, Angela H. A. M.; Mevius, Dik; Guerra, Beatriz; Mullany, Peter; Roberts, Adam Paul; Aarts, Henk J. M.

    2011-01-01

    In this review an overview is given on antibiotic resistance (AR) mechanisms with special attentions to the AR genes described so far preceded by a short introduction on the discovery and mode of action of the different classes of antibiotics. As this review is only dealing with acquired resistance, attention is also paid to mobile genetic elements such as plasmids, transposons, and integrons, which are associated with AR genes, and involved in the dispersal of antimicrobial determinants between different bacteria. PMID:22046172

  6. Realistic Earth matter effects and a method to acquire information about small θ13 in the detection of supernova neutrinos

    NASA Astrophysics Data System (ADS)

    Guo, Xin-Heng; Huang, Ming-Yang; Young, Bing-Lin

    2009-06-01

    In this paper, we first calculate the realistic Earth matter effects in the detection of type II supernova neutrinos at the Daya Bay reactor neutrino experiment which is currently under construction. It is found that the Earth matter effects depend on the neutrino incident angle θ, the neutrino mass hierarchy Δm312, the crossing probability at the high resonance region inside the supernova, PH, the neutrino temperature, Tα, and the pinching parameter in the neutrino spectrum, ηα. We also take into account the collective effects due to neutrino-neutrino interactions inside the supernova. With the expression for the dependence of PH on the neutrino mixing-angle θ13, we obtain the relations between θ13 and the event numbers for various reaction channels of supernova neutrinos. Using these relations, we propose a possible method to acquire information about θ13 smaller than 1.5°. Such a sensitivity cannot be achieved by the reactor neutrino deta at the Daya Bay experiment which has a sensitivity of the order of θ13˜3°. Furthermore, we apply this method to other neutrino experiments, i.e. Super-K, SNO, KamLAND, LVD, MinBooNE, Borexino, and Double-Chooz. We also study the energy spectra of the differential event numbers, dN/dE.

  7. The pathophysiology of acquired premature ejaculation.

    PubMed

    McMahon, Chris G; Jannini, Emmanuele A; Serefoglu, Ege C; Hellstrom, Wayne J G

    2016-08-01

    The second Ad Hoc International Society for Sexual Medicine (ISSM) Committee for the Definition of Premature Ejaculation defined acquired premature ejaculation (PE) as a male sexual dysfunction characterized by a the development of a clinically significant and bothersome reduction in ejaculation latency time in men with previous normal ejaculatory experiences, often to about 3 minutes or less, the inability to delay ejaculation on all or nearly all vaginal penetrations, and the presence of negative personal consequences, such as distress, bother, frustration and/or the avoidance of sexual intimacy. The literature contains a diverse range of biological and psychological etiological theories. Acquired PE is commonly due to sexual performance anxiety, psychological or relationship problems, erectile dysfunction (ED), and occasionally prostatitis and hyperthyroidism, consistent with the predominant organic etiology of acquired PE, men with this complaint are usually older, have a higher mean BMI and a greater incidence of comorbid disease including hypertension, sexual desire disorder, diabetes mellitus, chronic prostatitis, and ED compared to lifelong, variable and subjective PE. PMID:27652216

  8. The pathophysiology of acquired premature ejaculation

    PubMed Central

    Jannini, Emmanuele A.; Serefoglu, Ege C.; Hellstrom, Wayne J. G.

    2016-01-01

    The second Ad Hoc International Society for Sexual Medicine (ISSM) Committee for the Definition of Premature Ejaculation defined acquired premature ejaculation (PE) as a male sexual dysfunction characterized by a the development of a clinically significant and bothersome reduction in ejaculation latency time in men with previous normal ejaculatory experiences, often to about 3 minutes or less, the inability to delay ejaculation on all or nearly all vaginal penetrations, and the presence of negative personal consequences, such as distress, bother, frustration and/or the avoidance of sexual intimacy. The literature contains a diverse range of biological and psychological etiological theories. Acquired PE is commonly due to sexual performance anxiety, psychological or relationship problems, erectile dysfunction (ED), and occasionally prostatitis and hyperthyroidism, consistent with the predominant organic etiology of acquired PE, men with this complaint are usually older, have a higher mean BMI and a greater incidence of comorbid disease including hypertension, sexual desire disorder, diabetes mellitus, chronic prostatitis, and ED compared to lifelong, variable and subjective PE. PMID:27652216

  9. The pathophysiology of acquired premature ejaculation

    PubMed Central

    Jannini, Emmanuele A.; Serefoglu, Ege C.; Hellstrom, Wayne J. G.

    2016-01-01

    The second Ad Hoc International Society for Sexual Medicine (ISSM) Committee for the Definition of Premature Ejaculation defined acquired premature ejaculation (PE) as a male sexual dysfunction characterized by a the development of a clinically significant and bothersome reduction in ejaculation latency time in men with previous normal ejaculatory experiences, often to about 3 minutes or less, the inability to delay ejaculation on all or nearly all vaginal penetrations, and the presence of negative personal consequences, such as distress, bother, frustration and/or the avoidance of sexual intimacy. The literature contains a diverse range of biological and psychological etiological theories. Acquired PE is commonly due to sexual performance anxiety, psychological or relationship problems, erectile dysfunction (ED), and occasionally prostatitis and hyperthyroidism, consistent with the predominant organic etiology of acquired PE, men with this complaint are usually older, have a higher mean BMI and a greater incidence of comorbid disease including hypertension, sexual desire disorder, diabetes mellitus, chronic prostatitis, and ED compared to lifelong, variable and subjective PE.

  10. High Pressure Oxygen A-Band Spectra

    NASA Astrophysics Data System (ADS)

    Drouin, Brian; Sung, Keeyoon; Yu, Shanshan; Lunny, Elizabeth M.; Bui, Thinh Quoc; Okumura, Mitchio; Rupasinghe, Priyanka; Bray, Caitlin; Long, David A.; Hodges, Joseph; Robichaud, David; Benner, D. Chris; Devi, V. Malathy; Hoo, Jiajun

    2015-06-01

    Composition measurements from remote sensing platforms require knowledge of air mass to better than the desired precision of the composition. Oxygen spectra allow determination of air mass since the mixing ratio of oxygen is fixed. The OCO-2 mission is currently retrieving carbon dioxide concentration using the oxygen A-band for air mass normalization. The 0.25% accuracy desired for the carbon dioxide concentration has pushed the state-of-the-art for oxygen spectroscopy. To produce atmospheric pressure A-band cross-sections with this accuracy requires a sophisticated line-shape model (Galatry or Speed-Dependent) with line mixing (LM) and collision induced absorption (CIA). Models of each of these phenomena exist, but an integrated self-consistent model must be developed to ensure accuracy. This presentation will describe the ongoing effort to parameterize these phenomena on a representative data set created from complementary experimental techniques. The techniques include Fourier transform spectroscopy (FTS), photo-acoustic spectroscopy (PAS) and cavity ring-down spectroscopy (CRDS). CRDS data allow long-pathlength measurements with absolute intensities, providing lineshape information as well as LM and CIA, however the subtleties of the lineshape are diminished in the saturated line-centers. Conversely, the short paths and large dynamic range of the PAS data allow the full lineshape to be discerned, but with an arbitrary intensity axis. Finally, the FTS data provides intermediate paths and consistency across a broad pressure range. These spectra are all modeled with the Labfit software using first the spectral line database HITRAN, and then model values are adjusted and fitted for better agreement with the data.

  11. Mass spectrometry of aerospace materials

    NASA Technical Reports Server (NTRS)

    Colony, J. A.

    1976-01-01

    Mass spectrometry is used for chemical analysis of aerospace materials and contaminants. Years of analytical aerospace experience have resulted in the development of specialized techniques of sampling and analysis which are required in order to optimize results. This work has resulted in the evolution of a hybrid method of indexing mass spectra which include both the largest peaks and the structurally significant peaks in a concise format. With this system, a library of mass spectra of aerospace materials was assembled, including the materials responsible for 80 to 90 percent of the contamination problems at Goddard Space Flight Center during the past several years.

  12. The coupling of direct analysis in real time ionization to Fourier transform ion cyclotron resonance mass spectrometry for ultrahigh-resolution mass analysis.

    PubMed

    Rummel, Julia L; McKenna, Amy M; Marshall, Alan G; Eyler, John R; Powell, David H

    2010-03-01

    Direct Analysis in Real Time (DART) is an ambient ionization technique for mass spectrometry that provides rapid and sensitive analyses with little or no sample preparation. DART has been reported primarily for mass analyzers of low to moderate resolving power such as quadrupole ion traps and time-of-flight (TOF) mass spectrometers. In the current work, a custom-built DART source has been successfully coupled to two different Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers for the first time. Comparison of spectra of the isobaric compounds, diisopropyl methylphosphonate and theophylline, acquired by 4.7 T FT-ICR MS and TOF MS, demonstrates that the TOF resolving power can be insufficient for compositionally complex samples. 9.4 T FT-ICR MS yielded the highest mass resolving power yet reported with DART ionization for 1,2-benzanthracene and 9,10-diphenylanthracene. Polycyclic aromatic hydrocarbons exhibit a spatial dependence in ionization mechanisms between the DART source and the mass spectrometer. The feasibility of analyzing a variety of samples was established with the introduction and analysis of food products and crude oil samples. DART FT-ICR MS provides complex sample analysis that is rapid, highly selective and information-rich, but limited to relatively low-mass analytes.

  13. Rapid Identification of the Foodborne Pathogen Trichinella spp. by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry.

    PubMed

    Mayer-Scholl, Anne; Murugaiyan, Jayaseelan; Neumann, Jennifer; Bahn, Peter; Reckinger, Sabine; Nöckler, Karsten

    2016-01-01

    Human trichinellosis occurs through consumption of raw or inadequately processed meat or meat products containing larvae of the parasitic nematodes of the genus Trichinella. Currently, nine species and three genotypes are recognized, of which T. spiralis, T. britovi and T. pseudospiralis have the highest public health relevance. To date, the differentiation of the larvae to the species and genotype level is based primarily on molecular methods, which can be relatively time consuming and labor intensive. Due to its rapidness and ease of use a matrix assisted laser desorption / ionization time of flight mass spectrometry (MALDI-TOF MS) reference spectra database using Trichinella strains of all known species and genotypes was created. A formicacid/acetonitrile protein extraction was carried out after pooling 10 larvae of each Trichinella species and genotype. Each sample was spotted 9 times using α-cyano 4-hydoxy cinnamic acid matrix and a MicroFlex LT mass spectrometer was used to acquire 3 spectra (m/z 2000 to 20000 Da) from each spot resulting in 27 spectra/species or genotype. Following the spectra quality assessment, Biotyper software was used to create a main spectra library (MSP) representing nine species and three genotypes of Trichinella. The evaluation of the spectra generated by MALDI-TOF MS revealed a classification which was comparable to the results obtained by molecular methods. Also, each Trichinella species utilized in this study was distinct and distinguishable with a high confidence level. Further, different conservation methods such as freezing and conservation in alcohol and the host species origin of the isolated larvae did not have a significant influence on the generated spectra. Therefore, the described MALDI-TOF MS can successfully be implemented for both genus and species level identification and represents a major step forward in the use of this technique in foodborne parasitology.

  14. Rapid Identification of the Foodborne Pathogen Trichinella spp. by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

    PubMed Central

    Mayer-Scholl, Anne; Murugaiyan, Jayaseelan; Neumann, Jennifer; Bahn, Peter; Reckinger, Sabine; Nöckler, Karsten

    2016-01-01

    Human trichinellosis occurs through consumption of raw or inadequately processed meat or meat products containing larvae of the parasitic nematodes of the genus Trichinella. Currently, nine species and three genotypes are recognized, of which T. spiralis, T. britovi and T. pseudospiralis have the highest public health relevance. To date, the differentiation of the larvae to the species and genotype level is based primarily on molecular methods, which can be relatively time consuming and labor intensive. Due to its rapidness and ease of use a matrix assisted laser desorption / ionization time of flight mass spectrometry (MALDI-TOF MS) reference spectra database using Trichinella strains of all known species and genotypes was created. A formicacid/acetonitrile protein extraction was carried out after pooling 10 larvae of each Trichinella species and genotype. Each sample was spotted 9 times using α-cyano 4-hydoxy cinnamic acid matrix and a MicroFlex LT mass spectrometer was used to acquire 3 spectra (m/z 2000 to 20000 Da) from each spot resulting in 27 spectra/species or genotype. Following the spectra quality assessment, Biotyper software was used to create a main spectra library (MSP) representing nine species and three genotypes of Trichinella. The evaluation of the spectra generated by MALDI-TOF MS revealed a classification which was comparable to the results obtained by molecular methods. Also, each Trichinella species utilized in this study was distinct and distinguishable with a high confidence level. Further, different conservation methods such as freezing and conservation in alcohol and the host species origin of the isolated larvae did not have a significant influence on the generated spectra. Therefore, the described MALDI-TOF MS can successfully be implemented for both genus and species level identification and represents a major step forward in the use of this technique in foodborne parasitology. PMID:26999436

  15. Complex Spectra in Fusion Plasmas

    NASA Astrophysics Data System (ADS)

    von Hellermann, M. G.; Bertschinger, G.; Biel, W.; Giroud, C.; Jaspers, R.; Jupen, C.; Marchuk, O.; O'Mullane, M.; Summers, H. P.; Whiteford, A.; Zastrow, K.-D.

    2005-01-01

    The need for quantitative evaluation of complex line emission spectra as observed in hot fusion plasmas initiated a challenging development of sophisticated interpretation tools based on integrating advanced atomic modelling with detailed treatment of the plasma environment. The successful merging of the two worlds has led to routine diagnostic procedures which have contributed enormously to the understanding of underlying plasma processes and also to a wide acceptance of spectroscopy as a reliable diagnostic method. In this paper three characteristic types of spectra of current and continuing interest are presented. The first is that of medium/heavy species with many ionisation stages revealed in survey VUV and XUV spectra. Such species occur as control gases, as wall materials, as ablated heavy species and possible as layered wall dopants for monitoring erosion. The spectra are complex with line-like and quasi-continuum regions and are amenable to advanced `pattern recognition' methods. The second type is of few electron, highly ionised systems observed as line-of-sight integrated passive emission spectra in the soft x-ray region. They are analysed successfully in terms of plasma parameters through matching of observation with predicted synthetic spectra. Examples used here include highly resolved helium-like emission spectra of argon, iron and titanium observed on the tokamaks TEXTOR and Tore Supra. The third type, and the emphasis of this work, comprises spectra linked to active beam spectroscopy, that is, charge exchange recombination spectroscopy (CXRS) and beam emission spectroscopy (BES). In this case, a complex spectrum is again composed of a (usually) dominating active spectrum and an underlying passive emission spectrum. Its analysis requires modelling of both active and passive features. Examples used here are from the CXRS diagnostic at JET and TEXTOR. They display characteristic features of the main light impurity ions (C+6, He+2, N+7, Ne+10 and Ar+18

  16. Distinguishing Vaccinium species by chemical fingerprinting based on NMR spectra, validated with spectra collected in different laboratories.

    PubMed

    Markus, Michelle A; Ferrier, Jonathan; Luchsinger, Sarah M; Yuk, Jimmy; Cuerrier, Alain; Balick, Michael J; Hicks, Joshua M; Killday, K Brian; Kirby, Christopher W; Berrue, Fabrice; Kerr, Russell G; Knagge, Kevin; Gödecke, Tanja; Ramirez, Benjamin E; Lankin, David C; Pauli, Guido F; Burton, Ian; Karakach, Tobias K; Arnason, John T; Colson, Kimberly L

    2014-06-01

    A method was developed to distinguish Vaccinium species based on leaf extracts using nuclear magnetic resonance spectroscopy. Reference spectra were measured on leaf extracts from several species, including lowbush blueberry (Vaccinium angustifolium), oval leaf huckleberry (Vaccinium ovalifolium), and cranberry (Vaccinium macrocarpon). Using principal component analysis, these leaf extracts were resolved in the scores plot. Analysis of variance statistical tests demonstrated that the three groups differ significantly on PC2, establishing that the three species can be distinguished by nuclear magnetic resonance. Soft independent modeling of class analogies models for each species also showed discrimination between species. To demonstrate the robustness of nuclear magnetic resonance spectroscopy for botanical identification, spectra of a sample of lowbush blueberry leaf extract were measured at five different sites, with different field strengths (600 versus 700 MHz), different probe types (cryogenic versus room temperature probes), different sample diameters (1.7 mm versus 5 mm), and different consoles (Avance I versus Avance III). Each laboratory independently demonstrated the linearity of their NMR measurements by acquiring a standard curve for chlorogenic acid (R(2) = 0.9782 to 0.9998). Spectra acquired on different spectrometers at different sites classifed into the expected group for the Vaccinium spp., confirming the utility of the method to distinguish Vaccinium species and demonstrating nuclear magnetic resonance fingerprinting for material validation of a natural health product. PMID:24963620

  17. Distinguishing Vaccinium species by chemical fingerprinting based on NMR spectra, validated with spectra collected in different laboratories.

    PubMed

    Markus, Michelle A; Ferrier, Jonathan; Luchsinger, Sarah M; Yuk, Jimmy; Cuerrier, Alain; Balick, Michael J; Hicks, Joshua M; Killday, K Brian; Kirby, Christopher W; Berrue, Fabrice; Kerr, Russell G; Knagge, Kevin; Gödecke, Tanja; Ramirez, Benjamin E; Lankin, David C; Pauli, Guido F; Burton, Ian; Karakach, Tobias K; Arnason, John T; Colson, Kimberly L

    2014-06-01

    A method was developed to distinguish Vaccinium species based on leaf extracts using nuclear magnetic resonance spectroscopy. Reference spectra were measured on leaf extracts from several species, including lowbush blueberry (Vaccinium angustifolium), oval leaf huckleberry (Vaccinium ovalifolium), and cranberry (Vaccinium macrocarpon). Using principal component analysis, these leaf extracts were resolved in the scores plot. Analysis of variance statistical tests demonstrated that the three groups differ significantly on PC2, establishing that the three species can be distinguished by nuclear magnetic resonance. Soft independent modeling of class analogies models for each species also showed discrimination between species. To demonstrate the robustness of nuclear magnetic resonance spectroscopy for botanical identification, spectra of a sample of lowbush blueberry leaf extract were measured at five different sites, with different field strengths (600 versus 700 MHz), different probe types (cryogenic versus room temperature probes), different sample diameters (1.7 mm versus 5 mm), and different consoles (Avance I versus Avance III). Each laboratory independently demonstrated the linearity of their NMR measurements by acquiring a standard curve for chlorogenic acid (R(2) = 0.9782 to 0.9998). Spectra acquired on different spectrometers at different sites classifed into the expected group for the Vaccinium spp., confirming the utility of the method to distinguish Vaccinium species and demonstrating nuclear magnetic resonance fingerprinting for material validation of a natural health product.

  18. Distinguishing Vaccinium Species by Chemical Fingerprinting Based on NMR Spectra, Validated with Spectra Collected in Different Laboratories

    PubMed Central

    Markus, Michelle A.; Ferrier, Jonathan; Luchsinger, Sarah M.; Yuk, Jimmy; Cuerrier, Alain; Balick, Michael J.; Hicks, Joshua M.; Killday, K. Brian; Kirby, Christopher W.; Berrue, Fabrice; Kerr, Russell G.; Knagge, Kevin; Gödecke, Tanja; Ramirez, Benjamin E.; Lankin, David C.; Pauli, Guido F.; Burton, Ian; Karakach, Tobias K.; Arnason, John T.; Colson, Kimberly L.

    2014-01-01

    A method was developed to distinguish Vaccinium species based on leaf extracts using nuclear magnetic resonance spectroscopy. Reference spectra were measured on leaf extracts from several species, including lowbush blueberry (Vaccinium angustifolium), oval leaf huckleberry (Vaccinium ovalifolium), and cranberry (Vaccinium macrocarpon). Using principal component analysis, these leaf extracts were resolved in the scores plot. Analysis of variance statistical tests demonstrated that the three groups differ significantly on PC2, establishing that the three species can be distinguished by nuclear magnetic resonance. Soft independent modeling of class analogies models for each species also showed discrimination between species. To demonstrate the robustness of nuclear magnetic resonance spectroscopy for botanical identification, spectra of a sample of lowbush blueberry leaf extract were measured at five different sites, with different field strengths (600 versus 700 MHz), different probe types (cryogenic versus room temperature probes), different sample diameters (1.7 mm versus 5 mm), and different consoles (Avance I versus Avance III). Each laboratory independently demonstrated the linearity of their NMR measurements by acquiring a standard curve for chlorogenic acid (R2 = 0.9782 to 0.9998). Spectra acquired on different spectrometers at different sites classifed into the expected group for the Vaccinium spp., confirming the utility of the method to distinguish Vaccinium species and demonstrating nuclear magnetic resonance fingerprinting for material validation of a natural health product. PMID:24963620

  19. Access to experimentally infeasible spectra by pure-shift NMR covariance

    NASA Astrophysics Data System (ADS)

    Fredi, André; Nolis, Pau; Cobas, Carlos; Parella, Teodor

    2016-09-01

    Covariance processing is a versatile processing tool to generate synthetic NMR spectral representations without the need to acquire time-consuming experimental datasets. Here we show that even experimentally prohibited NMR spectra can be reconstructed by introducing key features of a reference 1D CHn-edited spectrum into standard 2D spectra. This general procedure is illustrated with the calculation of experimentally infeasible multiplicity-edited pure-shift NMR spectra of some very popular homonuclear (ME-psCOSY and ME-psTOCSY) and heteronuclear (ME-psHSQC-TOCSY and ME-psHMBC) experiments.

  20. Access to experimentally infeasible spectra by pure-shift NMR covariance.

    PubMed

    Fredi, André; Nolis, Pau; Cobas, Carlos; Parella, Teodor

    2016-09-01

    Covariance processing is a versatile processing tool to generate synthetic NMR spectral representations without the need to acquire time-consuming experimental datasets. Here we show that even experimentally prohibited NMR spectra can be reconstructed by introducing key features of a reference 1D CHn-edited spectrum into standard 2D spectra. This general procedure is illustrated with the calculation of experimentally infeasible multiplicity-edited pure-shift NMR spectra of some very popular homonuclear (ME-psCOSY and ME-psTOCSY) and heteronuclear (ME-psHSQC-TOCSY and ME-psHMBC) experiments.

  1. Analysis of photometric spectra of 17 meteors

    NASA Technical Reports Server (NTRS)

    Millman, P. M.

    1982-01-01

    The initial phase of the photometry which involved 17 meteor spectra consisting of eight Geminid spectra, six Orionid spectra and three Eta Aquarid spectra is discussed. Among these 17 spectra it is found that the Geminid spectra are of the best quality and are used for the identification of the atomic lines and molecular bands that normally appear on video tape spectra. The data from the Geminid records are used for developing calibration techniques in photometry. The Orionid and Eta Aquarid spectra are chosen for early analysis because of the current interest in all physical and chemical data relating to Comet Halley.

  2. Rapid discrimination of bacteria using a miniature mass spectrometer.

    PubMed

    Pulliam, Christopher J; Wei, Pu; Snyder, Dalton T; Wang, Xiao; Ouyang, Zheng; Pielak, Rafal M; Graham Cooks, R

    2016-03-01

    Bacteria colonies were analyzed using paper spray ionization coupled with a portable mass spectrometer. The spectra were averaged and processed using multivariate analysis to discriminate between different species of bacteria based on their unique phospholipid profiles. Full scan mass spectra and product ion MS/MS data were compared to those recorded using a benchtop linear ion trap mass spectrometer. PMID:26844973

  3. Mass Spectrometry of Large, Fragile, and Involatile Molecules.

    ERIC Educational Resources Information Center

    Busch, Kenneth L.; Cooks, R. Graham

    1982-01-01

    Desorption ionization (DI) is used to obtain mass spectra of molecules whose vaporization by heating may lead to thermal degradation. Discusses DI techniques, characteristics of DI mass spectra, ion production, current applications of DI in mass spectroscopy, developments in DI, and prospects for future evolution of new DI techniques. (Author/JN)

  4. Predicting charmonium and bottomonium spectra with a quark harmonic oscillator

    NASA Technical Reports Server (NTRS)

    Norbury, J. W.; Badavi, F. F.; Townsend, L. W.

    1986-01-01

    The nonrelativistic quark model is applied to heavy (nonrelativistic) meson (two-body) systems to obtain sufficiently accurate predictions of the spin-averaged mass levels of the charmonium and bottomonium spectra as an example of the three-dimensional harmonic oscillator. The present calculations do not include any spin dependence, but rather, mass values are averaged for different spins. Results for a charmed quark mass value of 1500 MeV/c-squared show that the simple harmonic oscillator model provides good agreement with experimental values for 3P states, and adequate agreement for the 3S1 states.

  5. Scaling and universality in microbial size spectra

    NASA Astrophysics Data System (ADS)

    Giometto, A.; Altermatt, F.; Carrara, F.; Maritan, A.; Rinaldo, A.

    2012-12-01

    In this work, focus is placed on the mass distribution of individual organisms of a given species in laboratory communities of protists. The relevance of the work pertains the importance of the variability of body size - currently neglected by most theoretical approaches or simply synthesized by the species' mean body mass - in a broad spectrum of issues ranging from the interpretation of Kleiber's law and of intertwined macroecological laws, to the ubiquity of broad, often scale-free community size spectra in nature. Here, it is shown experimentally that single species' size distributions for thirteen different protists' species spanning four orders of magnitude exhibit certain regularities well captured by a finite-size scaling distribution. In fact, once suitably rescaled, they collapse onto the same distribution regardless of the vast differences in their size. This is found to apply over four orders of magnitude in mass, thus suggesting the existence of an underlying universal mechanism shaping the size distribution of such organisms. In addition, the theoretical origins of the experimental result are addressed and a simple model of cell growth and division is shown to account for the main features of the observed universality. Environmental forcing of various kinds is shown not to affect the scaling result. It is claimed that this work provides a significant contribution to a number of open problems in ecology, like for instance the long-lasting dispute on linked scaling exponents in macroecological empirical relations. In fact, the characterization of the fluctuations in the mass of organisms enters directly several ecological scaling laws and the embedded account for whole size distributions (as opposed to mean body mass alone) acts as the explanatory variable for a number of current debates.

  6. AVIRIS spectra of California wetlands

    NASA Technical Reports Server (NTRS)

    Gross, Michael F.; Ustin, Susan L.; Klemas, Vytautas

    1988-01-01

    Spectral data gathered by the AVIRIS from wetlands in the Suisun Bay area of California on 13 October 1987 were analyzed. Spectra representing stands of numerous vegetation types (including Sesuvium verrucosum, Scirpus acutus and Scirpus californicus, Xanthium strumarium, Cynadon dactylon, and Distichlis spicata) and soil were isolated. Despite some defects in the data, it was possible to detect vegetation features such as differences in the location of the chlorophyll red absorption maximum. Also, differences in cover type spectra were evident in other spectral regions. It was not possible to determine if the observed features represent noise, variability in canopy architecture, or chemical constituents of leaves.

  7. Acquired prosopagnosia without word recognition deficits.

    PubMed

    Susilo, Tirta; Wright, Victoria; Tree, Jeremy J; Duchaine, Bradley

    2015-01-01

    It has long been suggested that face recognition relies on specialized mechanisms that are not involved in visual recognition of other object categories, including those that require expert, fine-grained discrimination at the exemplar level such as written words. But according to the recently proposed many-to-many theory of object recognition (MTMT), visual recognition of faces and words are carried out by common mechanisms [Behrmann, M., & Plaut, D. C. ( 2013 ). Distributed circuits, not circumscribed centers, mediate visual recognition. Trends in Cognitive Sciences, 17, 210-219]. MTMT acknowledges that face and word recognition are lateralized, but posits that the mechanisms that predominantly carry out face recognition still contribute to word recognition and vice versa. MTMT makes a key prediction, namely that acquired prosopagnosics should exhibit some measure of word recognition deficits. We tested this prediction by assessing written word recognition in five acquired prosopagnosic patients. Four patients had lesions limited to the right hemisphere while one had bilateral lesions with more pronounced lesions in the right hemisphere. The patients completed a total of seven word recognition tasks: two lexical decision tasks and five reading aloud tasks totalling more than 1200 trials. The performances of the four older patients (3 female, age range 50-64 years) were compared to those of 12 older controls (8 female, age range 56-66 years), while the performances of the younger prosopagnosic (male, 31 years) were compared to those of 14 younger controls (9 female, age range 20-33 years). We analysed all results at the single-patient level using Crawford's t-test. Across seven tasks, four prosopagnosics performed as quickly and accurately as controls. Our results demonstrate that acquired prosopagnosia can exist without word recognition deficits. These findings are inconsistent with a key prediction of MTMT. They instead support the hypothesis that face

  8. Acquired prosopagnosia without word recognition deficits.

    PubMed

    Susilo, Tirta; Wright, Victoria; Tree, Jeremy J; Duchaine, Bradley

    2015-01-01

    It has long been suggested that face recognition relies on specialized mechanisms that are not involved in visual recognition of other object categories, including those that require expert, fine-grained discrimination at the exemplar level such as written words. But according to the recently proposed many-to-many theory of object recognition (MTMT), visual recognition of faces and words are carried out by common mechanisms [Behrmann, M., & Plaut, D. C. ( 2013 ). Distributed circuits, not circumscribed centers, mediate visual recognition. Trends in Cognitive Sciences, 17, 210-219]. MTMT acknowledges that face and word recognition are lateralized, but posits that the mechanisms that predominantly carry out face recognition still contribute to word recognition and vice versa. MTMT makes a key prediction, namely that acquired prosopagnosics should exhibit some measure of word recognition deficits. We tested this prediction by assessing written word recognition in five acquired prosopagnosic patients. Four patients had lesions limited to the right hemisphere while one had bilateral lesions with more pronounced lesions in the right hemisphere. The patients completed a total of seven word recognition tasks: two lexical decision tasks and five reading aloud tasks totalling more than 1200 trials. The performances of the four older patients (3 female, age range 50-64 years) were compared to those of 12 older controls (8 female, age range 56-66 years), while the performances of the younger prosopagnosic (male, 31 years) were compared to those of 14 younger controls (9 female, age range 20-33 years). We analysed all results at the single-patient level using Crawford's t-test. Across seven tasks, four prosopagnosics performed as quickly and accurately as controls. Our results demonstrate that acquired prosopagnosia can exist without word recognition deficits. These findings are inconsistent with a key prediction of MTMT. They instead support the hypothesis that face

  9. Women and the Acquired Immunodeficiency Syndrome

    PubMed Central

    Wofsy, Constance B.

    1988-01-01

    SPECIAL EDITOR'S NOTE: Constance B. Wofsy, MD, is Co-Director of AIDS Activities at San Francisco General Hospital and Medical Center, as well as Associate Clinical Professor of Medicine at the University of California, San Francisco; Assistant Chief, Infectious Diseases, San Francisco General Hospital; and Principal Investigator, Project AWARE (Association for Women's AIDS Research and Education). Although she was not able to contribute an article for WOMEN AND MEDICINE on this very important subject, she kindly agreed to an interview. Both physicians and nonphysicians were asked what questions they had about the acquired immunodeficiency syndrome (AIDS) and the human immunodeficiency virus (HIV) in women. Images PMID:3250110

  10. Psychological issues in acquired facial trauma

    PubMed Central

    De Sousa, Avinash

    2010-01-01

    The face is a vital component of one’s personality and body image. There are a vast number of variables that influence recovery and rehabilitation from acquired facial trauma many of which are psychological in nature. The present paper presents the various psychological issues one comes across in facial trauma patients. These may range from body image issues to post-traumatic stress disorder symptoms accompanied by anxiety and depression. Issues related to facial and body image affecting social life and general quality of life are vital and the plastic surgeon should be aware of such issues and competent to deal with them in patients and families. PMID:21217982

  11. Triple arthrodesis for adult acquired flatfoot.

    PubMed

    Catanzariti, Alan R; Dix, Brian T; Richardson, Phillip E; Mendicino, Robert W

    2014-07-01

    The primary goal of triple arthrodesis for stage III and IV adult acquired flatfoot is to obtain a well-aligned plantigrade foot that will support the ankle in optimal alignment. Ancillary procedures including posterior muscle group lengthening, medial displacement calcaneal osteotomy, medial column stabilization, peroneus brevis tenotomy, or transfer and harvest of regional bone graft are often necessary to achieve adequate realignment. Image intensification is helpful in confirming optimal realignment before fixation. Results of triple arthrodesis are enhanced with adequate preparation of joint surfaces, bone graft/orthobiologics, 2-point fixation of all 3 tritarsal joints, and a vertical heel position.

  12. Acquired progressive lymphangioma of the nipple

    PubMed Central

    Alkhalili, Eyas; Ayoubieh, Houriya; O'Brien, William; Billings, Steven D

    2014-01-01

    A 47-year-old woman presented with left nipple itch and discomfort. On physical examination she was found to have a 7 mm lesion. She underwent bilateral mammography and bilateral breast ultrasound which were normal. A punch biopsy of the lesion was performed in the office and the specimen submitted to pathology. Histopathological examination showed ectatic vascular spaces lined by flattened, cytologically bland endothelial cells dissecting the dermal collagen. Evident lymphatic valves were present within the vascular spaces confirming that the vessels were lymphatic in nature. The diagnosis of acquired progressive lymphangioma (benign lymphangioendothelioma) was rendered. PMID:25246470

  13. Acquired scalp alopecia. Part II: A review.

    PubMed

    Sullivan, J R; Kossard, S

    1999-05-01

    The neutrophil-associated and infiltrative scarring alopecias are reviewed including folliculitis decalvans, tufted folliculitis, dissecting cellulitis of the scalp, acne keloidalis and follicular degeneration syndrome. The management of acquired scalp alopecia is also reviewed including newer, promising therapies. More specific agents targeting components of the androgen system will make the treatment of androgenetic alopecia more rewarding. Similarly new immunomodulatory therapies show great promise for the lymphocyte-associated alopecias and include a new generation of macrolide immunosuppressives (tacrolimus, SDZ ASM 981, and SDZ 281-240), some of which appear to have good transcutaneous absorption. PMID:10333615

  14. Origins of species: acquired genomes and individuality

    NASA Technical Reports Server (NTRS)

    Margulis, L.

    1993-01-01

    Entire genomes with their accompanying protein synthetic systems are transferred throughout the biosphere primarily as bacteria and protists which become symbionts as they irreversibly integrate into pre-existing organisms to form more complex individuals. Individualization is stabilized by simultaneous transmission of once-separate heterologous genetic systems. The origin of new species is hypothesized to correlate with the acquisition, integration and subsequent inheritance of such acquired microbial genomes. These processes were recognized by Mereschkovsky ("Symbiogenesis" in Russian, 1909) and by Wallin ("Symbionticism", see p. 181, this issue).

  15. Origins of species: acquired genomes and individuality.

    PubMed

    Margulis, L

    1993-01-01

    Entire genomes with their accompanying protein synthetic systems are transferred throughout the biosphere primarily as bacteria and protists which become symbionts as they irreversibly integrate into pre-existing organisms to form more complex individuals. Individualization is stabilized by simultaneous transmission of once-separate heterologous genetic systems. The origin of new species is hypothesized to correlate with the acquisition, integration and subsequent inheritance of such acquired microbial genomes. These processes were recognized by Mereschkovsky ("Symbiogenesis" in Russian, 1909) and by Wallin ("Symbionticism", see p. 181, this issue).

  16. AGU acquires Springer-Verlag Series

    NASA Astrophysics Data System (ADS)

    AGU has acquired Springer-Verlag's (New York) Coastal and Estuarine Studies book series. This acquisition adds thirty-nine volumes to AGU's own Coastal and Estuarine Sciences book series.Coastal and estuarine science is a rapidly growing area of research driven in part by an increasing awareness of man's impact on the coastal zone, and the importance in understanding its delicate ecosystems. This area of study enhances AGU's initiatives in interdisciplinary research. Particular emphasis is being placed on understanding the complex interactions between the physical, geological, chemical, and biological aspects of marine science.

  17. Acquired Congenital Malalignment of the Great Toenails

    PubMed Central

    Decker, Ashley; Scher, Richard K.; Avarbock, Andrew

    2016-01-01

    Congenital malalignment is the lateral deviation of the nail plate along the longitudinal axis due to the lateral rotation of the nail matrix. The nail plate grows out in ridges caused by repeated microtrauma to the nail. Common complications include onychomycosis, Pseudomonas infection and acute or chronic paronychia. Treatment options range from conservative management to surgical options including realignment and nail matrixectomy. Congenital malalignment usually presents in infancy or childhood, but we present two cases of acquired malalignment occurring in the teenage years. PMID:27171597

  18. [Acquired cystic renal disease. Association with hypernephroma].

    PubMed

    Comesaña, E; Pesqueira, D; Tardáguila, F; De la Fuente, A; Antón, I; Vidal, L; Zungri, E

    1992-02-01

    Emergence of multiple bilateral renal cysts observed in patients undergoing periodic haemodialysis is 40%. The pathology, known as Acquired Cystic Renal Disease (A.C.R.D.) presents a high association to renal cancer. Two cases of A.C.R.D. and their association with hypernephroma, one resulting in secondary retroperitoneal haemorrhage and the other in intracystic haemorrhage, are presented. Forms and diagnosis are analyzed, insisting upon the need of monitoring the patients in haemodialysis from the point of view of tumour emergence.

  19. Near-Infrared Spectra of Supernovae

    NASA Astrophysics Data System (ADS)

    Gerardy, C. L.; Fesen, R. A.; Hoflich, P.; Nomoto, K.; Garnavich, P. M.; Jha, S.; Challis, P. M.; Kirshner, R. P.; Wheeler, J. C.; Sakai, S.

    2001-12-01

    We present results from a survey of the near-infrared properties of all types of supernovae. Near-infrared spectra of the subluminous Type Ia SN 1999by taken 5 days before to two weeks after maximum light have been analysed using self-consistent SN Ia explosion models. The data generally agree with 1D delayed-detonation models, indicate a near Chandrasekhar-mass WD progenitor, and show low yield of iron-peak elements confined to the innermost layers of the ejecta. This puts strong constraints on the mixing of large iron blobs into the outer layers due to Rayleigh-Taylor instabilities during the deflagration phase. NIR spectra of Type IIP SNe are relatively line-free during the plateau phase, showing largely hydrogen emission with only a handful of other lines, mostly in the 1-1.2 micron region. After the plateau phase, Type IIP spectra become much richer, showing many overlapping emission features throughout the near-infrared. It appears that CO emission is a common feature of core-collapse supernovae, as several detections of first overtone CO emission near 2.3 microns have been made, including SN 1998S (IIn), SN 1999em, SN 1999gi (IIP) and SN 2000ew (Ic). Finally, we find that Type IIn supernovae often exhibit extraordinary infrared excesses at late times. This is probably thermal emission from hot dust, most likely in the dense circumstellar gas surrounding the progenitor star. The infrared luminosity can reach 1041-42 erg s-1, and can last for several years. A possible scenario is that the dust emission is an ``infrared echo'' powered not by the flash of the SN explosion, but rather by UV/X-ray emission from the strong shock interaction with the dense circumstellar material.

  20. Variable interstellar lines in spectra of HD 73882

    NASA Astrophysics Data System (ADS)

    Galazutdinov, G.; Krełowski, J.; Beletsky, Y.; Valyavin, G.

    2013-11-01

    We report a detection of variability in interstellar absorption lines of Cai at 4227 Å and Fei at 3860 Å in very high signal-to-noise ratio (>1000) UVES and MIKE spectra of HD 73882 (NX Vel) carried out with the aid of 8-m telescope UT2 at Paranal and 6.5-m Magellan Telescope Clay at Las Campanas Observatory, Chile. The spectra, acquired in 2006 January and 2012 January, respectively, clearly show that the intensity and profile shapes of the Cai and Fei lines had dramatically changed within the 6 year period. Other interstellar features, observed along the same line of sight, do not demonstrate strong changes. It is likely that a high velocity CaFe cloud obscured the star between the two observations.

  1. Evidence for Partial Melting in Reflectance Spectra of 433 Eros

    NASA Technical Reports Server (NTRS)

    McFadden, L. A.; Goldman, Noah; Gaffey, M. J.; Izenberg, N. R.

    2005-01-01

    The NEAR Shoemaker spacecraft returned near-IR spectra of asteroid 433 Eros at spatial resolutions ranging from 2.5 to 100's km during its year-long orbital mission in 2000. Assuming modified Gaussian absorption bands represent the reflectance spectrum between 0.8-2.5 m we fit the average of all geometrically corrected spectra acquired by the near-IR spectrometer (NIS) with seven absorption bands. Interpretation of the absorption bands in terms of olivine and pyroxene minerals indicates that the surface of Eros contains olivine and two pyroxenes with compositions that are indicative of a partially melted assemblage. This partial melting must have occurred when the asteroid was part of a larger minor planet, prior to break up into its current elongated and irregular shape.

  2. Pentacene Derivatives: Electronic Structure and Spectra

    NASA Astrophysics Data System (ADS)

    Netusil, Ross; Ilie, Carolina; Kane, Thorin; Damkaci, Fehmi

    2013-03-01

    The variation in composition and structure of the substituent groups of pentacene compounds promises a broad range of electronic structures and behaviors and provides a vast and alluring field of inquiry with avenues of exploration. These include the development of synthetic schema, the process of design for novel derivatives and, in order to identify those hypothesized compounds which demonstrate the desired behavior, the identification and refinement of computational tools that make accurate predictions about the electronic behavior of theoretical compounds. Two computational techniques and six pentacene derivatives are here examined. One technique was used to predict the vibrational spectra of the compounds, in order to both acquire data about the optical conductivity of the compounds and to establish a pool of theoretical data against which experimental data will be compared. The molecular orbital energy level diagram of the same six compounds was derived using a second approach, with the same goals of discerning between valid and invalid predictive schema by comparison with pending experimental data and between hypothesized compounds which show promise and those which present little potential for use in organic semiconductor technology.

  3. AIS spectra of desert shrub canopies

    NASA Technical Reports Server (NTRS)

    Murray, R.; Isaacson, D. L.; Schrumpf, B. J.; Ripple, W. J.; Lewis, A. J.

    1986-01-01

    Airborne Imaging Spectrometer (AIS) data were collected 30 August 1985 from a desert shrub community in central Oregon. Spectra from artificial targets placed on the test site and from bare soil, big sagebrush (Artemesia tridentata wyomingensis), silver sagebrush (Artemesia cana bolander), and exposed volcanic rocks were studied. Spectral data from grating position 3 (tree mode) were selected from 25 ground positions for analysis by Principal Factor Analysis (PFA). In this grating position, as many as six factors were identified as significant in contributing to spectral structure. Channels 74 through 84 (tree mode) best characterized between-class differences. Other channels were identified as nondiscriminating and as associated with such errors as excessive atmospheric absorption and grating positin changes. The test site was relatively simple with the two species (A. tridentata and A. cana) representing nearly 95% of biomass and with only two mineral backgrounds, a montmorillonitic soil and volcanic rocks. If, as in this study, six factors of spectral structure can be extracted from a single grating position from data acquired over a simple vegetation community, then AIS data must be considered rich in information-gathering potential.

  4. SIEMENS ADVANCED QUANTRA FTICR MASS SPECTROMETER FOR ULTRA HIGH RESOLUTION AT LOW MASS

    SciTech Connect

    Spencer, W; Laura Tovo, L

    2008-07-08

    The Siemens Advanced Quantra Fourier Transform Ion Cyclotron Resonance (FTICR) mass spectrometer was evaluated as an alternative instrument to large double focusing mass spectrometers for gas analysis. High resolution mass spectrometers capable of resolving the common mass isomers of the hydrogen isotopes are used to provide data for accurate loading of reservoirs and to monitor separation of tritium, deuterium, and helium. Conventional double focusing magnetic sector instruments have a resolution that is limited to about 5000. The Siemens FTICR instrument achieves resolution beyond 400,000 and could possibly resolve the tritium ion from the helium-3 ion, which differ by the weight of an electron, 0.00549 amu. Working with Y-12 and LANL, SRNL requested Siemens to modify their commercial Quantra system for low mass analysis. To achieve the required performance, Siemens had to increase the available waveform operating frequency from 5 MHz to 40 MHz and completely redesign the control electronics and software. However, they were able to use the previous ion trap, magnet, passive pump, and piezo-electric pulsed inlet valve design. NNSA invested $1M in this project and acquired four systems, two for Y-12 and one each for SRNL and LANL. Siemens claimed a $10M investment in the Quantra systems. The new Siemens Advanced Quantra demonstrated phenomenal resolution in the low mass range. Resolution greater than 400,000 was achieved for mass 2. The new spectrometer had a useful working mass range to 500 Daltons. However, experiments found that a continuous single scan from low mass to high was not possible. Two useful working ranges were established covering masses 1 to 6 and masses 12 to 500 for our studies. A compromise performance condition enabled masses 1 to 45 to be surveyed. The instrument was found to have a dynamic range of about three orders of magnitude and quantitative analysis is expected to be limited to around 5 percent without using complex fitting algorithms

  5. Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra.

    SciTech Connect

    Frank, Ari M; Monroe, Matthew E; Shah, Anuj R; Carver, Jeremy J; Bandeira, Nuno; Moore, Ronald J; Anderson, Gordon A; Smith, Richard D; Pevzner, Pavel A

    2011-07-01

    Tandem mass spectrometry (MS/MS) experiments yield multiple, nearly identical spectra of the same peptide in various laboratories, but proteomics researchers typically do not leverage the unidentified spectra produced in other labs to decode spectra they generate. We propose a spectral archives approach that clusters MS/MS datasets, representing similar spectra by a single consensus spectrum. Spectral archives extend spectral libraries by analyzing both identified and unidentified spectra in the same way and maintaining information about peptide spectra that are common across species and conditions. Thus archives offer both traditional library spectrum similarity-based search capabilities along with new ways to analyze the data. By developing a clustering tool, MS-Cluster, we generated a spectral archive from ~1.18 billion spectra that greatly exceeds the size of existing spectral repositories. We advocate that publicly available data should be organized into spectral archives rather than be analyzed as disparate datasets, as is mostly the case today.

  6. Experimental access to HSQC spectra decoupled in all frequency dimensions

    NASA Astrophysics Data System (ADS)

    Sakhaii, Peyman; Haase, Burkhard; Bermel, Wolfgang

    2009-08-01

    A new operator called RESET "Reducing nuclEar Spin multiplicitiEs to singuleTs" is presented to acquire broadband proton decoupled proton spectra in one and two dimensions. Basically, the homonuclear decoupling is achieved through the application of bilinear rotation pulses and delays. A [BIRD] r,x pulse building block is used to selectively invert all proton magnetization remotely attached to 13C isotopes, which is equivalent to a scalar J decoupling of the protons directly attached to 13C from all other protons in the spin system. In conjunction with an appropriate data processing technique pure shift proton spectra are obtained. For this purpose, the concept of constant time acquisition in the observe dimension is exploited. Both ideas were merged together producing superior HSQC based pseudo 3D pulse sequences. The resulting HSQC spectra show cross peaks with collapsed multiplet structures and singlet responses for the proton chemical shift frequencies. An unambiguous assignment of signals from overcrowded spectra becomes much easier. Finally, the recently introduced SHARC technique is exploited to enhance the capability of the scalar J decoupling method. A significant reduction of the total measurement time is achieved. The time is saved by reducing the number of 13C chemical shift evolution increments and working with superimposed narrow spectral bandwidths in the 13C indirect domain.

  7. Principal Component Analysis of Arctic Solar Irradiance Spectra

    NASA Technical Reports Server (NTRS)

    Rabbette, Maura; Pilewskie, Peter; Gore, Warren J. (Technical Monitor)

    2000-01-01

    During the FIRE (First ISCPP Regional Experiment) Arctic Cloud Experiment and coincident SHEBA (Surface Heat Budget of the Arctic Ocean) campaign, detailed moderate resolution solar spectral measurements were made to study the radiative energy budget of the coupled Arctic Ocean - Atmosphere system. The NASA Ames Solar Spectral Flux Radiometers (SSFRs) were deployed on the NASA ER-2 and at the SHEBA ice camp. Using the SSFRs we acquired continuous solar spectral irradiance (380-2200 nm) throughout the atmospheric column. Principal Component Analysis (PCA) was used to characterize the several tens of thousands of retrieved SSFR spectra and to determine the number of independent pieces of information that exist in the visible to near-infrared solar irradiance spectra. It was found in both the upwelling and downwelling cases that almost 100% of the spectral information (irradiance retrieved from 1820 wavelength channels) was contained in the first six extracted principal components. The majority of the variability in the Arctic downwelling solar irradiance spectra was explained by a few fundamental components including infrared absorption, scattering, water vapor and ozone. PCA analysis of the SSFR upwelling Arctic irradiance spectra successfully separated surface ice and snow reflection from overlying cloud into distinct components.

  8. Gemini spectra of 12000 K white dwarf stars

    NASA Astrophysics Data System (ADS)

    Kepler, S. O.; Castanheira, B. G.; Costa, A. F. M.; Koester, D.

    2006-11-01

    We report signal-to-noise ratio (S/N) ~= 100 optical spectra for four DA white dwarf stars acquired with the GMOS spectrograph of the 8-m Gemini north telescope. These stars have 18 < g < 19 and are around Teff ~ 12000 K, where the hydrogen lines are close to maximum. Our purpose is to test if the effective temperatures and surface gravities derived from the relatively low-S/N ( ~ 21) optical spectra acquired by the Sloan Digital Sky Survey through model atmosphere fitting are trustworthy. Our spectra range from 3800 to 6000 Å, therefore including Hβ to H9. The H8 line was only marginally present in the SDSS spectra, but is crucial to determine the gravity. When we compare the values published by Kleinman et al. and Eisenstein et al. with our line-profile technique (LPT) fits, the average differences are: ΔTeff ~= 320 K, systematically lower in the SDSS, and Δ log g ~= 0.24 dex, systematically larger in the SDSS. The correlation between the gravity and the effective temperature can only be broken at wavelengths bluer than 3800 Å. The uncertainties in Teff are 60 per cent larger, and in log g larger by a factor of 4, than the internal uncertainties of Kleinman et al. and Eisenstein et al. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the Particle Physics and Astronomy Research Council (United Kingdom), the National Research Council (Canada), CONICYT (Chile), the Australian Research Council (Australia), CNPq (Brazil) and CONICET (Argentina). E-mail: kepler@if.ufrgs.br

  9. Spectra of Microwave Oscillations in Ferrospinel Films

    NASA Astrophysics Data System (ADS)

    Badrtdinov, G. S.; Mitlina, L. A.; Meleshko, N. V.

    2016-09-01

    The absorption spectra of ferrospinel single crystal films obtained by the method of chemical transport reactions are considered. It is demonstrated that along with a homogeneous resonance, additional absorption peaks corresponding to exchange spin modes localized in the surface layer are observed in the absorption spectrum investigated with an EPR spectrometer in the case of perpendicular orientation of the film with respect to an external static magnetic field. Resonant interaction of magnetostatic oscillations with exchange spin modes in the surface layer is detected in the case of tangent magnetization. The width of the magnetostatic layer and the ranges of existence of the surface and volume modes depend on the relationship between the constants of uniaxial surface anisotropy and crystallographic magnetic anisotropy. The wave numbers of the magnetostatic and exchange spin modes, the parameters of inhomogeneous exchange, and the effective magnon masses are calculated.

  10. Workshop to establish databases of carbohydrate spectra

    SciTech Connect

    1995-12-31

    The workshop was organized to formulate guidelines for establishing spectral databases of complex carbohydrates. The databases will enable the scientific community to avoid the great waste of research effort and funds that frequently occurs when carbohydrate chemists are forced to duplicate the structural characterization of previously characterized complex carbohydrates. Chemists waste their effort on repetitive characterizations because in the absence of spectral databases they are unaware they are analyzing a known molecule until they have completely determined its structure. Chemists will be able to avoid much of this wasted effort when the collections of mass and of nuclear magnetic resonance (NMR) spectra initiated at the workshop are subsequently developed into searchable databases. Then scientists only need query the databases with the spectrum or with information defining the spectrum of an unidentified carbohydrate to find out if it has been previously characterized.

  11. cloud supersaturations and CCN spectra

    NASA Astrophysics Data System (ADS)

    Hudson, James; Noble, Stephen

    2014-05-01

    Multiple regression analysis predictions of low altitude cloud droplet concentrations based on measured CCN spectra compared much better with measured low altitude droplet concentrations than various CCN concentrations at single supersaturations (S) in two aircraft cumulus cloud projects, RICO and ICE-T. The addition of vertical velocity (W) to the single and multiple regressions showed small improvements. For RICO the multiple regression correlations were also superior to previous adiabatic model predictions of droplet concentrations also based on CCN spectra and mean W. More adiabatic cloud parcels showed only slightly better correlations than flight-averaged droplet concentrations. Results show the value of more extensive CCN spectra and the relative unimportance of W variations for determining droplet concentrations in these Caribbean cumuli. The fact that flight-averaged droplet concentrations of all low cloud data was almost as well correlated with CCN spectra as were droplet concentrations of more adiabatic cloud parcels indicates that entrainment did not significantly perturb CCN-droplet concentration relationships. As should be expected higher cloud S were determined for the cumulus clouds than for stratus clouds. Suppression of cloud S by higher CCN concentrations that had previously been observed in stratus was observed in ICE-T but not in RICO where the CCN range may have been too low for cloud S suppression. But ICE-T and a stratus project, POST, even showed this S suppression over the same limited maritime CCN range as RICO.

  12. Classical Trajectories and Quantum Spectra

    NASA Technical Reports Server (NTRS)

    Mielnik, Bogdan; Reyes, Marco A.

    1996-01-01

    A classical model of the Schrodinger's wave packet is considered. The problem of finding the energy levels corresponds to a classical manipulation game. It leads to an approximate but non-perturbative method of finding the eigenvalues, exploring the bifurcations of classical trajectories. The role of squeezing turns out decisive in the generation of the discrete spectra.

  13. Asian elephants acquire inaccessible food by blowing.

    PubMed

    Mizuno, Kaori; Irie, Naoko; Hiraiwa-Hasegawa, Mariko; Kutsukake, Nobuyuki

    2016-01-01

    Many animals acquire otherwise inaccessible food with the aid of sticks and occasionally water. As an exception, some reports suggest that elephants manipulate breathing through their trunks to acquire inaccessible food. Here, we report on two female Asian elephants (Elephas maximus) in Kamine Zoo, Japan, who regularly blew to drive food within their reach. We experimentally investigated this behaviour by placing foods in inaccessible places. The elephants blew the food until it came within accessible range. Once the food was within range, the elephants were increasingly less likely to blow as the distance to the food became shorter. One subject manipulated her blowing duration based on food distance: longer when the food was distant. These results suggest that the elephants used their breath to achieve goals: that is, they used it not only to retrieve the food but also to fine-tune the food position for easy grasping. We also observed individual differences in the elephants' aptitude for this technique, which altered the efficiency of food acquisition. Thus, we added a new example of spontaneous behaviour for achieving a goal in animals. The use of breath to drive food is probably unique to elephants, with their dexterous trunks and familiarity with manipulating the act of blowing, which is commonly employed for self-comfort and acoustic communication.

  14. Asian elephants acquire inaccessible food by blowing.

    PubMed

    Mizuno, Kaori; Irie, Naoko; Hiraiwa-Hasegawa, Mariko; Kutsukake, Nobuyuki

    2016-01-01

    Many animals acquire otherwise inaccessible food with the aid of sticks and occasionally water. As an exception, some reports suggest that elephants manipulate breathing through their trunks to acquire inaccessible food. Here, we report on two female Asian elephants (Elephas maximus) in Kamine Zoo, Japan, who regularly blew to drive food within their reach. We experimentally investigated this behaviour by placing foods in inaccessible places. The elephants blew the food until it came within accessible range. Once the food was within range, the elephants were increasingly less likely to blow as the distance to the food became shorter. One subject manipulated her blowing duration based on food distance: longer when the food was distant. These results suggest that the elephants used their breath to achieve goals: that is, they used it not only to retrieve the food but also to fine-tune the food position for easy grasping. We also observed individual differences in the elephants' aptitude for this technique, which altered the efficiency of food acquisition. Thus, we added a new example of spontaneous behaviour for achieving a goal in animals. The use of breath to drive food is probably unique to elephants, with their dexterous trunks and familiarity with manipulating the act of blowing, which is commonly employed for self-comfort and acoustic communication. PMID:26541597

  15. Eye movement correlates of acquired central dyslexia.

    PubMed

    Schattka, Kerstin I; Radach, Ralph; Huber, Walter

    2010-08-01

    Based on recent progress in theory and measurement techniques, the analysis of eye movements has become one of the major methodological tools in experimental reading research. Our work uses this approach to advance the understanding of impaired information processing in acquired central dyslexia of stroke patients with aphasia. Up to now there has been no research attempting to analyze both word-based viewing time measures and local fixation patterns in dyslexic readers. The goal of the study was to find out whether specific eye movement parameters reflect pathologically preferred segmental reading in contrast to lexical reading. We compared oral reading of single words of normal controls (n=11) with six aphasic participants (two cases of deep, surface and residual dyslexia each). Participants were asked to read aloud lines of target words differing in length and frequency. Segmental reading was characterized by deviant spatial distribution of saccadic landing positions with initial fixations located mainly at the beginning of the word, while lexical readers showed the normative 'preferred landing positions' left to the center of the words. Contrary to expectation, word length did not distinguish between segmental and lexical readers, while word frequency showed the expected effect for lexical readers only. Their mean fixation duration was already prolonged during first pass reading reflecting their attempts of immediate access to lexical information. After first pass reading, re-reading time was significantly increased in all participants with acquired central dyslexia due to their exceedingly higher monitoring demands for oral reading.

  16. Acquiring functional object knowledge through motor imagery?

    PubMed

    Paulus, Markus; van Elk, Michiel; Bekkering, Harold

    2012-04-01

    A widely investigated question in the research on the acquisition of novel functional object representations is the role of the action system. Whereas most studies so far have investigated the role of active action training on the acquisition of object representation, we investigated whether people are able to acquire object representations by just imagining the use of novel objects, given that previous findings suggested that executed and imagined actions share a common representational format. To this end, participants trained the use of novel objects in a motor imagery condition. Training comprised the particular grip applied to the objects and the objects' typical end location. Subsequently, participants' object representations were assessed by means of an object detection task. The results show that participants responded slower when the novel objects were presented at functionally incorrect end locations, indicating that the participants had acquired functional knowledge about object use. Yet, there was no effect of correct versus incorrect grip. Altogether, the findings suggest that motor imagery can facilitate the acquisition of novel object representations, but point also to differences between first-hand action training and training by imagery.

  17. Shape effects on asteroid spectra

    NASA Astrophysics Data System (ADS)

    Davalos, J.; Carvano, J.

    2014-07-01

    The objective of this work is to probe how the shape of a body like an asteroid could be modifying its observed spectra and the derived mineralogical interfaces based on spectral modeling. To model this effect, we construct an oblate ellipsoid with triangular facets, where each facet contributes to the overall reflectance. The synthetic spectra is generated by the isotropic multiple-scattering approximation (IMSA) reflectance model of Hapke (1993). First, we obtained optical constants by inverting the spectra of meteorites, obtained from the RELAB spectral database. These optical constants were found inverting the reflectance bidirectional equation of Hapke; this is made in two steps: (i) The first inversion is to find the single-scattering albedo π (ii) in the model of Hapke, this albedo is found under the regime of the geometric optics, where the particle size is much larger than the wavelength of the incident radiation. Here we assumed a constant value for the real part of the optical constant n=1.5. With these optical constants, we can construct synthetic spectra for any particle size. The phase function used is the double Henyey-Greenstein phase function and an accurate expression for the H-functions. We started with the ellipsoidal shape a=1.0, b=c=0.5 for two particle size 50 and 250 μ m, in this part, we found good differences in the BAR parameter between the two geometric models, this was done for 100 Eucrite meteorites spectra. In this first study, we found that the BAR parameter between the two models is bigger when the particle size increases. In the second part, we started with different ellipsoidal shapes and produced synthetic spectra for material with eucrite and diogenite composition with a phase angle of 20 degrees, incidence and emission angles of 10 degrees, and particle size at 250 μ m. All spectra was generated for four parameters of phase angle b=[0.2,0.4,0.6,0.8] taking the empirical relation between the phase constants of Hapke (2012

  18. Digitally synthesized high purity, high-voltage radio frequency drive electronics for mass spectrometry.

    PubMed

    Schaefer, R T; MacAskill, J A; Mojarradi, M; Chutjian, A; Darrach, M R; Madzunkov, S M; Shortt, B J

    2008-09-01

    Reported herein is development of a quadrupole mass spectrometer controller (MSC) with integrated radio frequency (rf) power supply and mass spectrometer drive electronics. Advances have been made in terms of the physical size and power consumption of the MSC, while simultaneously making improvements in frequency stability, total harmonic distortion, and spectral purity. The rf power supply portion of the MSC is based on a series-resonant LC tank, where the capacitive load is the mass spectrometer itself, and the inductor is a solenoid or toroid, with various core materials. The MSC drive electronics is based on a field programmable gate array (FPGA), with serial peripheral interface for analog-to-digital and digital-to-analog converter support, and RS232/RS422 communications interfaces. The MSC offers spectral quality comparable to, or exceeding, that of conventional rf power supplies used in commercially available mass spectrometers; and as well an inherent flexibility, via the FPGA implementation, for a variety of tasks that includes proportional-integral derivative closed-loop feedback and control of rf, rf amplitude, and mass spectrometer sensitivity. Also provided are dc offsets and resonant dipole excitation for mass selective accumulation in applications involving quadrupole ion traps; rf phase locking and phase shifting for external loading of a quadrupole ion trap; and multichannel scaling of acquired mass spectra. The functionality of the MSC is task specific, and is easily modified by simply loading FPGA registers or reprogramming FPGA firmware. PMID:19044454

  19. Digitally synthesized high purity, high-voltage radio frequency drive electronics for mass spectrometry

    SciTech Connect

    Schaefer, R. T.; Mojarradi, M.; MacAskill, J. A.; Chutjian, A.; Darrach, M. R.; Madzunkov, S. M.; Shortt, B. J.

    2008-09-15

    Reported herein is development of a quadrupole mass spectrometer controller (MSC) with integrated radio frequency (rf) power supply and mass spectrometer drive electronics. Advances have been made in terms of the physical size and power consumption of the MSC, while simultaneously making improvements in frequency stability, total harmonic distortion, and spectral purity. The rf power supply portion of the MSC is based on a series-resonant LC tank, where the capacitive load is the mass spectrometer itself, and the inductor is a solenoid or toroid, with various core materials. The MSC drive electronics is based on a field programmable gate array (FPGA), with serial peripheral interface for analog-to-digital and digital-to-analog converter support, and RS232/RS422 communications interfaces. The MSC offers spectral quality comparable to, or exceeding, that of conventional rf power supplies used in commercially available mass spectrometers; and as well an inherent flexibility, via the FPGA implementation, for a variety of tasks that includes proportional-integral derivative closed-loop feedback and control of rf, rf amplitude, and mass spectrometer sensitivity. Also provided are dc offsets and resonant dipole excitation for mass selective accumulation in applications involving quadrupole ion traps; rf phase locking and phase shifting for external loading of a quadrupole ion trap; and multichannel scaling of acquired mass spectra. The functionality of the MSC is task specific, and is easily modified by simply loading FPGA registers or reprogramming FPGA firmware.

  20. Preliminary Analysis of AIS Spectral Data Acquired from Semi-arid Shrub Communities in the Owens Valley, California

    NASA Technical Reports Server (NTRS)

    Ustin, S. L.; Rock, B. N.

    1985-01-01

    Spectral characteristics of semic-arid plant communities using 128 channel airborne imaging spectrometer (AIS) data acquired on October 30, 1984. Both field and AIS spectra of vegetation were relatively featureless and differed from substrate spectra primarily in albedo. Unvegetated sand dunes were examined to assess spectral variation resulting from topographic irregularity. Although shrub cover as low as 10% could be detected on relatively flat surfaces, such differences were obscured in more heterogeneous terrain. Sagebrush-covered fans which had been scarred by fire were studied to determine the effect of changes in plant density on reflectance. Despite noise in the atmospherically corrected spectra, these provide better resolution of differences in plant density than spectra which are solar-corrected only. A high negative correlation was found between reflectance and plant cover in areas which had uniform substrates and vegetation types. A lower correlation was found where vegetation and substrates were more diverse.

  1. Model Atmospheres and X-Ray Spectra of Bursting Neutron Stars: Hydrogen-Helium Comptonized Spectra

    NASA Astrophysics Data System (ADS)

    Madej, J.; Joss, P. C.; Różańska, A.

    2004-02-01

    Compton scattering plays a crucial role in determining the structure of the atmosphere of an X-ray burster and its theoretical spectrum. Our paper presents a description of the plane-parallel model atmosphere of a very hot neutron star and its theoretical flux spectrum of outgoing radiation. Our model equations take into account all bound-free and free-free monochromatic opacities relevant to hydrogen-helium chemical composition and take into account the effects of Compton scattering of radiation in thermal plasma with fully relativistic thermal velocities. We use Compton scattering terms in the equation of transfer, which precisely describe photon-electron energy and momentum exchange for photons with initial energies exceeding the electron rest mass of 511 keV. Model atmosphere equations are solved with the variable Eddington factors technique. The grid of H-He model atmospheres and flux spectra is computed on a dense mesh of 107K<=Teff<=3×107K and a surface gravity of logg. In many cases, the assumed logg approached the critical gravity loggcr, i.e., the Eddington limit. We confirm that H-He spectra of X-ray bursters deviate from blackbody spectra and discuss their shapes. The table of color to effective temperature ratios shows that theoretical values of Tc/Teff do not exceed 1.9 in H-He atmospheres in hydrostatic and radiative equilibrium.

  2. Source spectra of seismic hum

    NASA Astrophysics Data System (ADS)

    Nishida, Kiwamu

    2014-10-01

    The observation of seismic hum from 2 to 20 mHz, also known as Earth's background free oscillations, has been established. Recent observations by broad-band seismometers show simultaneous excitation of Love waves (fundamental toroidal modes) and Rayleigh waves (fundamental spheroidal modes). The excitation amplitudes above 10 mHz can be explained by random shear traction sources on Earth's surface. With estimated source distributions, the most likely excitation mechanism is a linear coupling between ocean infragravity waves and seismic surface waves through seafloor topography. Observed Love and Rayleigh wave amplitudes below 5 mHz suggest that surface pressure sources could also contribute to their excitations, although the amplitudes have large uncertainties due to the high noise levels of the horizontal components. To quantify the observation, we develop a new method for estimation of the source spectra of random tractions on Earth's surface by modelling cross-spectra between pairs of stations. The method is to calculate synthetic cross-spectra for spatially isotropic and homogeneous excitations by random shear traction and pressure sources, and invert them with the observed cross-spectra to obtain the source spectra. We applied this method to the IRIS, ORFEUS, and F-net records from 618 stations with three components of broad-band seismometers for 2004-2011. The results show the dominance of shear traction above 5 mHz, which is consistent with past studies. Below 5 mHz, however, the spectral amplitudes of the pressure sources are comparable to those of shear traction. Observed acoustic resonance between the atmosphere and the solid Earth at 3.7 and 4.4 mHz suggests that atmospheric disturbances are responsible for the surface pressure sources, although non-linear ocean wave processes are also candidates for the pressure sources. Excitation mechanisms of seismic hum should be considered as a superposition of the processes of the solid Earth, atmosphere and ocean

  3. Accurate mass - time tag library for LC/MS-based metabolite profiling of medicinal plants

    PubMed Central

    Cuthbertson, Daniel J.; Johnson, Sean R.; Piljac-Žegarac, Jasenka; Kappel, Julia; Schäfer, Sarah; Wüst, Matthias; Ketchum, Raymond E. B.; Croteau, Rodney B.; Marques, Joaquim V.; Davin, Laurence B.; Lewis, Norman G.; Rolf, Megan; Kutchan, Toni M.; Soejarto, D. Doel; Lange, B. Markus

    2013-01-01

    We report the development and testing of an accurate mass – time (AMT) tag approach for the LC/MS-based identification of plant natural products (PNPs) in complex extracts. An AMT tag library was developed for approximately 500 PNPs with diverse chemical structures, detected in electrospray and atmospheric pressure chemical ionization modes (both positive and negative polarities). In addition, to enable peak annotations with high confidence, MS/MS spectra were acquired with three different fragmentation energies. The LC/MS and MS/MS data sets were integrated into online spectral search tools and repositories (Spektraris and MassBank), thus allowing users to interrogate their own data sets for the potential presence of PNPs. The utility of the AMT tag library approach is demonstrated by the detection and annotation of active principles in 27 different medicinal plant species with diverse chemical constituents. PMID:23597491

  4. Quantum confinement in metal nanofilms: Optical spectra

    NASA Astrophysics Data System (ADS)

    Khmelinskii, Igor; Makarov, Vladimir I.

    2016-05-01

    We report optical absorption and photoluminescence spectra of Au, Fe, Co and Ni polycrystalline nanofilms in the UV-vis-NIR range, featuring discrete bands resulting from transverse quantum confinement. The film thickness ranged from 1.1 to 15.6 nm, depending on the material. The films were deposited on fused silica substrates by sputtering/thermo-evaporation, with Fe, Co and Ni protected by a SiO2 film deposited on top. The results are interpreted within the particle-in-a-box model, with the box width equal to the mass thickness of the nanofilm. The transverse-quantized energy levels and transition energies scale as the inverse square of the film thickness. The calculated values of the effective electron mass are 0.93 (Au), 0.027 (Fe), 0.21 (Co) and 0.16 (Ni), in units of mo - the mass of the free electron, being independent on the film thickness. The uncertainties in the effective mass values are ca. 2.5%, determined by the film thickness calibration. The second calculated model parameter, the quantum number n of the HOMO, was thickness-independent in Au (5.00) and Fe (6.00), and increased with the film thickness in Co (from 7 to 9) and Ni (from 7 to 11). The transitions observed in the absorbance all start at the level n and correspond to Δn=+1, +2, +3, etc. The photoluminescence bands exhibit large Stokes shifts, shifting to higher energies with the increased excitation energy. The photoluminescence quantum yields grow linearly with the excitation energy, showing evidence of multiple exciton generation. A prototype Fe-SnO2 nanofilm photovoltaic cell demonstrated at least 90% quantum yield of photoelectrons at 77 K.

  5. Osteoporosis: Peak Bone Mass in Women

    MedlinePlus

    ... higher in men than in women. Before puberty, boys and girls acquire bone mass at similar rates. After puberty, ... teenage boys to get enough calcium. Physical Activity. Girls and boys and young adults who exercise regularly generally achieve ...

  6. Phobos surface spectra mineralogical modeling

    NASA Astrophysics Data System (ADS)

    Pajola, M.; Lazzarin, M.; Dalle Ore, C. M.; Cruikshank, D. P.; Roush, T. L.; Pendleton, Y.; Bertini, I.; Magrin, S.; Carli, C.; La Forgia, F.; Barbieri, C.

    2014-04-01

    A mineralogical model composed of a mixture of Tagish Lake meteorite (TL) and Pyroxene Glass (PM80) was presented in [1] to explain the surface reflectance of Phobos from 0.25 to 4.0 μm. The positive results we obtained, when comparing the OSIRIS data [2] extended in wavelength to include the [3,4] spectra, forced us to perform a wider comparison between our TL-PM80 model and the CRISM and OMEGA Phobos spectra presented in [5]. Such spectra cover three different regions of interest (ROIs) situated in the Phobos sub-Mars hemisphere: the interior of the Stickney crater, its eastern rim, and its proximity terrain southeast of the Reldresal crater. We decided to vary the percentage mixture of the components of our model (80% TL, 20% PM80), between pure TL and pure PM80, by means of the radiative transfer code based on the [6] formulation of the slab approximation. Once this spectral range was derived, see Fig. 1, we attempted to compare it with the [5] spectra between 0.4 and 2.6 μm, i.e. below the thermal emitted radiation, to see if any spectral match was possible. We observed that CRISM scaled spectra above 1.10 μm fall within pure Tagish Lake composition and the [1] model. The CRISM data below 1.10 μm present more discrepancies with our models, in particular for the Stickney's rim spectrum. Nevertheless the TL and PM80 components seem to be good mineralogical candidates on Phobos. We performed the same analysis with the OMEGA data and, again, we found out that the Stickney's rim spectrum lies out of our model range, while the two remaining spectra still lie between pure TL and 80% TL - 20% PM80, but indicating that a different, more complicated mixture is expected in order to explain properly both the spectral trend and the possible absorption bands located above 2.0 μm. Within this analysis, we point out that a big fraction of TL material (modeled pure or present with a minimum percentage of 80% mixed together with 20% PM80) seems to explain Phobos spectral

  7. Acquiring case adaptation knowledge: A hybrid approach

    SciTech Connect

    Leake, D.B.; Kinley, A.; Wilson, D.

    1996-12-31

    The ability of case-based reasoning (CBR) systems to apply cases to novel situations depends on their case adaptation knowledge. However, endowing CBR systems with adequate adaptation knowledge has proven to be a very difficult task. This paper describes a hybrid method for performing case adaptation, using a combination of rule-based and case-based reasoning. It shows how this approach provides a framework for acquiring flexible adaptation knowledge from experiences with autonomous adaptation and suggests its potential as a basis for acquisition of adaptation knowledge from interactive user guidance. It also presents initial experimental results examining the benefits of the approach and comparing the relative contributions of case learning and adaptation learning to reasoning performance.

  8. Acquire CoOmmodities Easily Card

    1998-05-29

    Acquire Commodities Easily Card (AceCard) provides an automated end-user method to distribute company credit card charges to internal charge numbers. AceCard will allow cardholders to record card purchases in an on-line order log, enter multiple account distributions per order that can be posted to the General Ledger, track orders, and receipt information, and provide a variety of cardholder and administrative reports. Please note: Customers must contact Ed Soler (423)-576-6151, Lockheed Martin Energy Systems, for helpmore » with the installation of the package. The fee for this installation help will be coordinated by the customer and Lockheed Martin and is in addition to cost of the package from ESTSC. Customers should contact Sandy Presley (423)-576-4708 for user help.« less

  9. Acquired alexia: lessons from successful treatment.

    PubMed

    Beeson, P M; Insalaco, D

    1998-11-01

    Two individuals with anomic aphasia and acquired alexia were each provided treatment for their reading impairment. Although reading of single words in isolation was fairly accurate, their text reading was slow and effortful, including functor substitutions and semantic errors. Prior to treatment, reading reaction times for single words showed grammatical class and word-length effects. Both patients responded positively to a treatment protocol that included two phases: (1) multiple oral rereading of text, and (2) reading phrase-formatted text that had increased spacing between phrasal clauses. Their reading rates for text improved while maintaining good comprehension. Following treatment, reading reaction times for single words showed the elimination of grammatical class and word-length effects, suggesting improved access to word forms, particularly functors.

  10. Acquire CoOmmodities Easily Card

    SciTech Connect

    Soler, E. E.

    1998-05-29

    Acquire Commodities Easily Card (AceCard) provides an automated end-user method to distribute company credit card charges to internal charge numbers. AceCard will allow cardholders to record card purchases in an on-line order log, enter multiple account distributions per order that can be posted to the General Ledger, track orders, and receipt information, and provide a variety of cardholder and administrative reports. Please note: Customers must contact Ed Soler (423)-576-6151, Lockheed Martin Energy Systems, for help with the installation of the package. The fee for this installation help will be coordinated by the customer and Lockheed Martin and is in addition to cost of the package from ESTSC. Customers should contact Sandy Presley (423)-576-4708 for user help.

  11. Acquired loss of red cell Kell antigens.

    PubMed

    Vengelen-Tyler, V; Gonzalez, B; Garratty, G; Kruppe, C; Johnson, C L; Mueller, K A; Marsh, W L

    1987-02-01

    A 19-year-old patient with a long history of idiopathic thrombocytopenic purpura developed a potent antibody against a high-incidence antigen in the Kell blood group system. The direct antiglobulin test on his red cells was negative. His cells exhibited profound depression of Kell blood group antigens, but antigens of other blood groups were normal. Transfusion of incompatible blood was well tolerated and differential agglutination tests, using selected Rh antisera, showed in vivo survival of the transfused red cells for more than 8 weeks. However, the transfused red cells also showed acquired loss of Kell antigens. Five months after the initial findings, Kell-related antibody disappeared and Kell antigens reappeared on his red cells. The patient's serum stored from the initial investigation now reacted with his freshly collected red cells. These data suggest that an environmental agent in the patient's plasma was responsible for the temporary loss of Kell antigens from red cells in his circulation.

  12. Stereotypic movement disorder after acquired brain injury.

    PubMed

    McGrath, Cynthia M; Kennedy, Richard E; Hoye, Wayne; Yablon, Stuart A

    2002-05-01

    Stereotypic movement disorder (SMD) consists of repetitive, non-functional motor behaviour that interferes with daily living or causes injury to the person. It is most often described in patients with mental retardation. However, recent evidence indicates that this condition is common among otherwise normal individuals. This case study describes a patient with new-onset SMD occurring after subdural haematoma and brain injury. SMD has rarely been reported after acquired brain injury, and none have documented successful treatment. The current psychiatric literature regarding neurochemistry, neuroanatomy, and treatment of SMD are reviewed with particular application to one patient. Treatment options include serotonin re-uptake inhibitors, opioid antagonists and dopamine antagonists. SMD has been under-appreciated in intellectually normal individuals, and may also be unrecognized after brain injury. Further investigation is needed in this area, which may benefit other individuals with SMD as well.

  13. The acquired immunodeficiency syndrome in gay men.

    PubMed

    Jaffe, H W; Hardy, A M; Morgan, W M; Darrow, W W

    1985-11-01

    The acquired immunodeficiency syndrome (AIDS) is a major health problem for gay men in the United States. About three fourths of all reported cases have occurred in this population, and the number is projected to double in the next year. In Manhattan and San Francisco, AIDS is now the leading cause of premature mortality in men aged 25 to 44 years who have never married. In a sample of a cohort of gay men enrolled in a San Francisco clinic, 2.7% of the men had the syndrome and 26% had related conditions in 1984. Antibody to human T-lymphotropic virus, type III/lymphadenopathy-associated virus was found in sera from 67% of the men, including 58% of asymptomatic men. Behavioral factors associated with an increased risk of AIDS include large numbers of sexual partners, receptive anal intercourse, and "fisting." The adoption of safer lifestyles is currently the basis of attempts to control the syndrome in gay men.

  14. Signal regulators of systemic acquired resistance

    PubMed Central

    Gao, Qing-Ming; Zhu, Shifeng; Kachroo, Pradeep; Kachroo, Aardra

    2015-01-01

    Salicylic acid (SA) is an important phytohormone that plays a vital role in a number of physiological responses, including plant defense. The last two decades have witnessed a number of breakthroughs related to biosynthesis, transport, perception and signaling mediated by SA. These findings demonstrate that SA plays a crictical role in both local and systemic defense responses. Systemic acquired resistance (SAR) is one such SA-dependent response. SAR is a long distance signaling mechanism that provides broad spectrum and long-lasting resistance to secondary infections throughout the plant. This unique feature makes SAR a highly desirable trait in crop production. This review summarizes the recent advances in the role of SA in SAR and discusses its relationship to other SAR inducers. PMID:25918514

  15. Acquired immunodeficiency syndrome: Ga-67 citrate imaging

    SciTech Connect

    Woolfenden, J.M.; Carrasquillo, J.A.; Larson, S.M.; Simmons, J.T.; Masur, H.; Smith, P.D.; Shelhamer, J.H.; Ognibene, F.P.

    1987-02-01

    All gallium-67 citrate scans obtained in patients with acquired immunodeficiency syndrome (AIDS) at the Clinical Center, National Institutes of Health (Bethesda, Md.) were retrospectively analyzed and correlated with the results of bronchoscopy, chest radiography, and endoscopy. There were 164 scans of 95 patients. Twenty scans were from patients with Pneumocystis carinii pneumonia; 19 were abnormal, for a sensitivity of 95%. Ga-67 uptake tended to be less in patients receiving therapy for P. carinii pneumonia. Chest radiographs were normal at least initially in three patients with abnormal scans and P. carinii pneumonia. Unusually prominent colonic activity was associated with infection in some patients. No lesions of Kaposi sarcoma showed tracer uptake. Gallium scanning is useful for detecting P. carinii pneumonia and other opportunistic infections in patients with AIDS, but it is not useful for localizing Kaposi sarcoma.

  16. Antihelper T cell autoantibody in acquired agammaglobulinemia.

    PubMed Central

    Rubinstein, A; Sicklick, M; Mehra, V; Rosen, F S; Levey, R H

    1981-01-01

    A patient with acquired agammaglobulinemia had an antihelper T cell factor that was identified as an immunoglobulin of the IgG class. The factor specifically bound to the TH2- T cell subset and, in the presence of complement, abolished the helper effect of normal T cells. The antihelper T cell antibody preceded by several years the appearance of suppressor TH2+Ia+ T cells, at which time the clinical course rapidly deteriorated. Plasmapheresis resulted in lymphocytosis and reappearance of a functionally intact helper T cell population. It did not affect the suppressor cells. Conversely, total thymectomy resulted in a temporary disappearance of the TH2+Ia+ suppressor cells, but did not decrease the levels of the autoantibody to helper T cells. Neither of these treatments reversed the state of agammaglobulinemia. PMID:6450224

  17. Acquired methaemoglobinaemia related to phenazopyridine ingestion.

    PubMed

    Shahani, Lokesh; Sattovia, Stacy

    2012-09-17

    Methaemoglobin is an altered state of haemoglobin in which the ferrous ions of haeme are oxidised to the ferric state. This results in increased affinity to the bound oxygen and decreasing its availability to tissues. Most cases of methaemoglobinaemia are acquired, resulting from an increased methaemoglobin formation by various exogenous agents. The authors report an elderly patient presenting to the emergency department with a 1-month history of shortness of breath. Around the same time she had started using over-the-counter (OTC) phenazopyridine tablets for urinary symptoms. The patient was hypoxic and cyanotic; however, lacked evidence of hypoxaemia on the arterial blood gas. The presence of abnormal haemoglobin was suspected and confirmed by elevated levels of methaemoglobin. Phenazopyridine was proposed to be the likely aetiology of the methaemoglobinaemia, which the patient was not aware of. This case highlights the importance of always inquiring the OTC drug use especially in geriatric population.

  18. Acquired methaemoglobinaemia related to phenazopyridine ingestion

    PubMed Central

    Shahani, Lokesh; Sattovia, Stacy

    2012-01-01

    Methaemoglobin is an altered state of haemoglobin in which the ferrous ions of haeme are oxidised to the ferric state. This results in increased affinity to the bound oxygen and decreasing its availability to tissues. Most cases of methaemoglobinaemia are acquired, resulting from an increased methaemoglobin formation by various exogenous agents. The authors report an elderly patient presenting to the emergency department with a 1-month history of shortness of breath. Around the same time she had started using over-the-counter (OTC) phenazopyridine tablets for urinary symptoms. The patient was hypoxic and cyanotic; however, lacked evidence of hypoxaemia on the arterial blood gas. The presence of abnormal haemoglobin was suspected and confirmed by elevated levels of methaemoglobin. Phenazopyridine was proposed to be the likely aetiology of the methaemoglobinaemia, which the patient was not aware of. This case highlights the importance of always inquiring the OTC drug use especially in geriatric population. PMID:22987905

  19. Multiple myeloma associated with acquired cutis laxa.

    PubMed

    Cho, S Y; Maguire, R F

    1980-08-01

    Acquired cutis laxa is a rare disorder characterized by diffuse laxity of the skin and loss of connective tissue support with involvement of the lungs, gastrointestinal tract, pelvic organs, and aorta. The case report presented herein describes a forty-six year old woman with multiple myeloma and cutis laxa. Her history included several severe allergic reactions and the gradual development of lax skin, loss of connective tissue support throughout the body, and emphysema. At autopsy, multiple myeloma, diffuse laxity of the skin, and panacinar emphysema were found. The amount of elastic fiber in the skin, lungs, and aorta was decreased and showed abnormal fragmentation. Results of direct immunofluorescence study demonstrated IgG bound to dermal elastic fibers. Speculation regarding an immunologic etiology of the elastic tissue abnormality is presented herein.

  20. Review of direct neutrino mass experiments

    SciTech Connect

    Dragoun, O.

    2015-10-28

    Advantages and drawbacks of the kinematic methods of the neutrino mass determination are discussed. The meaning of the effective neutrino mass, resulting from measurements of the endpoint region of β-spectra is clarified. Current experimental constraints on the mass of active as well as sterile neutrinos are presented. Several new experiments are briefly outlined.